title: single neuron, striatum, B12_10007015-OGC22-sal_1_D18__N419Barcode_722-515


title: single neuron, striatum, C09_10007015-OGC22-sal_1_L18__N419Barcode_722-520

status: Public on Nov 17 2019

type: SRA

city: San Francisco

first: Stephen

last: Quake

address: 499 Illinois St

country: USA

institute: Chan-Zuckerberg Biohub

description: single neuron isolated from mouse striatum

library_source: transcriptomic

data_processing:
Alignment (STAR v2.4.0) to mm10 mouse genome
Gene counting (HTSeq v0.11.1)
Normalization (log10 cpm + 1)
Removal of low quality cells (having < 1000 genes detected and <10^5 counts)
Genes scaled using Seurat v2.3.4 ScaleData
Genome_build: mm10
Supplementary_files_format_and_content: striatum_final.rds, striatum_raw_counts.csv

molecule: total RNA

organism: Mus musculus

source_name: striatum

extract_protocol:
Generation of D1-tdTom/D2-GFP, and D1-tomato BAC reporter mice was previously described(Gokce et al., 2016). All lines were maintained by backcrossing to C57Bl/6J. All other experiments were conducted on 5-7 week old male C57/Bl6 mice from Jackson Labs. Mice were weaned at ~21 days of age and housed in groups of 2-5 on a 12-hour light/dark cycle (lights on 0700-1900h), with free access to food. All procedures conformed to the National Institutes of Health Guidelines for the Care and Use of Laboratory Animals and were approved by the Stanford University. Parasagittal slices (350 μm) containing striatum were prepared using standard  procedures. Briefly, mice were anesthetized with isoflurane and decapitated,  brains were quickly removed and placed in ice-cold low-sodium/high-sucrose dissecting solution. Slices were cut by adhering the lateral surface of the brain to the stage of a Leica vibroslicer, and placed in ice-cold hibernate-A solution (Gibco, Themo Fisher). The striatum was dissected from each slice, and the tissue was dissociated using papain-based dissociation. Briefly, striatal tissue was incubated with frequent agitation at 30°C for 20 min 2mg/ml papain solution in Hibernate-A, followed by washing with hibernate-A including 1mg/ml Ovomucoid protease inhibitor (Sigma). The striatal slices were triturated briefly using fire polished glass Pasteur pipettes until a single-cell suspension was obtained. The suspension was cleaned from small debris by centrifuging for 3 min at 450g through a three-step density gradient of Percoll (Sigma), top layer containing small debris was discarded and remaining cells were pelleted for 5  min at 550g. The pellet was resuspended in 0.1 ml of hibernate A with DAPI (4’,6-diamidino-2-phenylindole, 1:4000 dilution; Sigma) to label dead cells(Gokce et al., 2016). Striatal tissue was kept in ice-cold solution throughout the processing except during the 20 min dissociation with papain at 30°C. Administrative Panel on Laboratory Animal Care. The dissociated cell suspension from adult D1-tdTom/D2-GFP mice was passed through a 70-μm cell strainer (BD Biosciences). Viable cells (DAPI negative) were sorted by FACS (Aria II; BD Biosciences). For specific enrichment of genetically labeled cell types, fluorescent striatal cells were analyzed to determine optimal parameters and gating for FACS. Finally, test sorted cells were imaged on confocal microscope as described previously(Gokce et al., 2016). Cells were sorted into ice-cold hibernate-A and pelleted by centrifugation for 5 min at 300g. Single cells were sorted into 96 well plates filled with 4 μl lysis buffer composed of 0.05% Triton X-100 (Sigma) and, ERCC spike-ins (1:24000000 dilution), 2.5 μM oligo-dT, 2.5 mM dNTP and 2U/μl of recombinant RNase inhibitor (Clontech) then spun down and frozen at -80°C. Plates were thawed and libraries prepared as described below.
96-well plates with sorted single cells were incubated for 3min at 72°C and immediately placed on ice. To perform reverse transcription (RT) we added each well a mix of 0.59μl H2O, 0.5μl SMARTScribe™ Reverse Transcriptase (Clontech), 2μl 5x First Strand buffer, 0.25μl Recombinant RNase Inhibitor (Clontech), 2μl Betaine (5M Sigma), 0.5μl DTT (100mM) 0.06μl MgCL2 (1M Sigma), 0.1μl Template-switching oligos (TSO) (100μM AAGCAGTGGTATCAACGCAGAGTACrGrG+G). Next reaction RT reaction mixes were incubated at 42°C for 90 min followed by 70°C for 5 min. Pre amplification of cDNA done by adding 12.5μl KAPA HiFi Hotstart 2x (KAPA Biosystems), 2.138μl H2O, 0.25μl ISPCR primers (10 μM, 5′-AAGCAGTGGTATCAACGCAGAGT-3), 0.1125μl Lambda Exonuclease under the following conditions: 37°C for 30 min, 95°C for 3 min, 21 cycles of (98°C for 20 sec, 67°C for 15 sec, 72°C for 4 min), final extension at 72°C for 5 min. Cells were then cleaned using 2 rounds of AMPure bead (Beckman-Coulter) cleanup at a 0.8:1 ratio of beads to PCR product. The cleaned cDNA was then tagmented using the Nextera XT DNA kit and following the included instructions, using 11 cycles of PCR to amplify the tagmented cDNA (Illumina). Tagmented cDNA was then pooled and analyzed with a Bioanalyzer 2100 High Sensitivity DNA kit (Agilent) to assure that >80%  of the product was in the 200-1000bp range. This process was repeated separately for each animal. Libaries were sequenced using 2x75 reads base pairs (bp) paired-end on Illumina HiSeq 2000 or NextSeq to a target depth of 1x10e6 reads/sample.

tag: nreads

tag: library

tag: subcluster

tag: tissue

value: striatum

tag: gender

value: male


title: single neuron, striatum, F12_10007015-OGC22-sal_1_M20__N419Barcode_724-510

value: MedShell


title: single neuron, striatum, G02_10007015-OGC22-sal_1_O20__N419Barcode_724-511


title: single neuron, striatum, F10_10007013-OGC20-sal_1_G10__N419Barcode_712-506


title: single neuron, striatum, F11_10007013-OGC20-sal_1_H10__N419Barcode_712-517

value: NAcc


title: single neuron, striatum, D09_10007013-OGC20-sal_1_N08__N419Barcode_710-521


title: single neuron, striatum, D11_10007013-OGC20-sal_1_P08__N419Barcode_710-522


title: single neuron, striatum, E10_10007015-OGC22-sal_1_A20__N419Barcode_724-502


title: single neuron, striatum, E02_10007015-OGC22-sal_1_K19__N419Barcode_723-508


title: single neuron, striatum, D03_10007015-OGC22-sal_1_B19__N419Barcode_723-513


title: single neuron, striatum, E03_10007013-OGC20-sal_1_D09__N419Barcode_711-515


title: single neuron, striatum, F01_10007013-OGC20-sal_1_N09__N419Barcode_711-521


title: single neuron, striatum, H04_10007013-OGC20-sal_1_H11__N419Barcode_714-517


title: single neuron, striatum, F05_10007013-OGC20-sal_1_B10__N419Barcode_712-513


title: single neuron, striatum, B12_10007017-OGC17-sal_1_F23__N419Barcode_728-516


title: single neuron, striatum, C09_10007013-OGC20-sal_1_B08__N419Barcode_710-513


title: single neuron, striatum, G08_10007013-OGC20-sal_1_P10__N419Barcode_712-522


title: single neuron, striatum, H10_10007015-OGC22-sal_1_M21__N419Barcode_726-510


title: single neuron, striatum, D12_10007015-OGC22-sal_1_J19__N419Barcode_723-518


title: single neuron, striatum, B05_10007017-OGC17-sal_1_O22__N419Barcode_727-511


title: single neuron, striatum, H10_10007013-OGC20-sal_1_N11__N419Barcode_714-521


title: single neuron, striatum, E07_10007013-OGC20-sal_1_H09__N419Barcode_711-517


title: single neuron, striatum, B12_10007013-OGC20-sal_1_I07__N419Barcode_707-507


title: single neuron, striatum, C05_10007017-OGC17-sal_1_K23__N419Barcode_728-508


title: single neuron, striatum, E02_10007017-OGC17-sal_1_O24__N419Barcode_729-511


title: single neuron, striatum, G11_10007013-OGC20-sal_1_C11__N419Barcode_714-503


title: single neuron, striatum, H01_10007015-OGC22-sal_1_H21__N419Barcode_726-517


title: single neuron, striatum, B07_10007015-OGC22-sal_1_P17__N419Barcode_721-522


title: single neuron, striatum, A11_10007015-OGC22-sal_1_J17__N419Barcode_721-518


title: single neuron, striatum, A10_10007017-OGC17-sal_1_H22__N419Barcode_727-517


title: single neuron, striatum, C03_10007015-OGC22-sal_1_F18__N419Barcode_722-516


title: single neuron, striatum, B04_10007017-OGC17-sal_1_N22__N419Barcode_727-521


title: single neuron, striatum, H02_10007013-OGC20-sal_1_F11__N419Barcode_714-516


title: single neuron, striatum, G07_10007015-OGC22-sal_1_C21__N419Barcode_726-503


title: single neuron, striatum, A04_10007013-OGC20-sal_1_E06__N419Barcode_706-505


title: single neuron, striatum, E04_10007013-OGC20-sal_1_E09__N419Barcode_711-505


title: single neuron, striatum, B06_10007017-OGC17-sal_1_P22__N419Barcode_727-522


title: single neuron, striatum, E08_10007013-OGC20-sal_1_I09__N419Barcode_711-507


title: single neuron, striatum, A10_10007013-OGC20-sal_1_K06__N419Barcode_706-508


title: single neuron, striatum, B06_10007013-OGC20-sal_1_C07__N419Barcode_707-503


title: single neuron, striatum, D12_10007017-OGC17-sal_1_M24__N419Barcode_729-510


title: single neuron, striatum, C11_10007017-OGC17-sal_1_P23__N419Barcode_728-522


title: single neuron, striatum, B10_10007015-OGC22-sal_1_C18__N419Barcode_722-503


title: single neuron, striatum, E01_10007013-OGC20-sal_1_B09__N419Barcode_711-513


title: single neuron, striatum, B11_10007013-OGC20-sal_1_H07__N419Barcode_707-517


title: single neuron, striatum, A07_10007015-OGC22-sal_1_G17__N419Barcode_721-506


title: single neuron, striatum, H03_10007013-OGC20-sal_1_G11__N419Barcode_714-506


title: single neuron, striatum, E09_10007015-OGC22-sal_1_P19__N419Barcode_723-522


title: single neuron, striatum, F12_10007013-OGC20-sal_1_I10__N419Barcode_712-507


title: single neuron, striatum, A02_10007013-OGC20-sal_1_C06__N419Barcode_706-503


title: single neuron, striatum, D05_10007017-OGC17-sal_1_F24__N419Barcode_729-516


title: single neuron, striatum, C07_10007013-OGC20-sal_1_P07__N419Barcode_707-522


title: single neuron, striatum, F01_10007015-OGC22-sal_1_D20__N419Barcode_724-515


title: single neuron, striatum, A11_10007013-OGC20-sal_1_L06__N419Barcode_706-520


title: single neuron, striatum, D03_10007017-OGC17-sal_1_D24__N419Barcode_729-515


title: single neuron, striatum, C08_10007015-OGC22-sal_1_K18__N419Barcode_722-508


title: single neuron, striatum, C07_10007015-OGC22-sal_1_J18__N419Barcode_722-518


title: single neuron, striatum, G02_10007013-OGC20-sal_1_K10__N419Barcode_712-508


title: single neuron, striatum, B04_10007015-OGC22-sal_1_M17__N419Barcode_721-510


title: single neuron, striatum, A09_10007017-OGC17-sal_1_G22__N419Barcode_727-506


title: single neuron, striatum, A08_10007017-OGC17-sal_1_F22__N419Barcode_727-516


title: single neuron, striatum, B01_10007017-OGC17-sal_1_K22__N419Barcode_727-508


title: single neuron, striatum, F09_10007015-OGC22-sal_1_K20__N419Barcode_724-508


title: single neuron, striatum, C03_10007013-OGC20-sal_1_L07__N419Barcode_707-520


title: single neuron, striatum, G10_10007013-OGC20-sal_1_B11__N419Barcode_714-513


title: single neuron, striatum, H07_10007013-OGC20-sal_1_K11__N419Barcode_714-508


title: single neuron, striatum, F04_10007015-OGC22-sal_1_G20__N419Barcode_724-506


title: single neuron, striatum, D05_10007015-OGC22-sal_1_D19__N419Barcode_723-515


title: single neuron, striatum, D01_10007017-OGC17-sal_1_B24__N419Barcode_729-513


title: single neuron, striatum, G06_10007013-OGC20-sal_1_N10__N419Barcode_712-521


title: single neuron, striatum, D10_10007017-OGC17-sal_1_K24__N419Barcode_729-508


title: single neuron, striatum, E02_10007018-NA_1_M06__N420Barcode_706-510


title: single neuron, striatum, H07_10007015-OGC22-sal_1_K21__N419Barcode_726-508


title: single neuron, striatum, C10_10007015-OGC22-sal_1_M18__N419Barcode_722-510


title: single neuron, striatum, B02_10007017-OGC17-sal_1_L22__N419Barcode_727-520


title: single neuron, striatum, A12_10007017-OGC17-sal_1_J22__N419Barcode_727-518


title: single neuron, striatum, B11_10007017-OGC17-sal_1_E23__N419Barcode_728-505


title: single neuron, striatum, G12_10007015-OGC22-sal_1_G21__N419Barcode_726-506


title: single neuron, striatum, C06_10007017-OGC17-sal_1_L23__N419Barcode_728-520


title: single neuron, striatum, C04_10007015-OGC22-sal_1_G18__N419Barcode_722-506


title: single neuron, striatum, G11_10007015-OGC22-sal_1_F21__N419Barcode_726-516


title: single neuron, striatum, B08_10007013-OGC20-sal_1_E07__N419Barcode_707-505


title: single neuron, striatum, G01_10007015-OGC22-sal_1_N20__N419Barcode_724-521


title: single neuron, striatum, B02_10007013-OGC20-sal_1_O06__N419Barcode_706-511


title: single neuron, striatum, D02_10007017-OGC17-sal_1_C24__N419Barcode_729-503


title: single neuron, striatum, F05_10007015-OGC22-sal_1_H20__N419Barcode_724-517


title: single neuron, striatum, H11_10007013-OGC20-sal_1_O11__N419Barcode_714-511


title: single neuron, striatum, A06_10007015-OGC22-sal_1_F17__N419Barcode_721-516


title: single neuron, striatum, A03_10007015-OGC22-sal_1_E17__N419Barcode_721-505


title: single neuron, striatum, B03_10007013-OGC20-sal_1_P06__N419Barcode_706-522


title: single neuron, striatum, D01_10007013-OGC20-sal_1_F08__N419Barcode_710-516


title: single neuron, striatum, H06_10007013-OGC20-sal_1_J11__N419Barcode_714-518


title: single neuron, striatum, A01_10007017-OGC17-sal_1_O21__N419Barcode_726-511


title: single neuron, striatum, B08_10007017-OGC17-sal_1_B23__N419Barcode_728-513


title: single neuron, striatum, E05_10007013-OGC20-sal_1_F09__N419Barcode_711-516


title: single neuron, striatum, H08_10007013-OGC20-sal_1_L11__N419Barcode_714-520


title: single neuron, striatum, C03_10007017-OGC17-sal_1_I23__N419Barcode_728-507


title: single neuron, striatum, H05_10007015-OGC22-sal_1_J21__N419Barcode_726-518


title: single neuron, striatum, F06_10007015-OGC22-sal_1_I20__N419Barcode_724-507


title: single neuron, striatum, F08_10007015-OGC22-sal_1_J20__N419Barcode_724-518


title: single neuron, striatum, G04_10007013-OGC20-sal_1_L10__N419Barcode_712-520


title: single neuron, striatum, A10_10007015-OGC22-sal_1_I17__N419Barcode_721-507


title: single neuron, striatum, B05_10007015-OGC22-sal_1_N17__N419Barcode_721-521


title: single neuron, striatum, C02_10007017-OGC17-sal_1_H23__N419Barcode_728-517


title: single neuron, striatum, D11_10007015-OGC22-sal_1_I19__N419Barcode_723-507


title: single neuron, striatum, B10_10007017-OGC17-sal_1_D23__N419Barcode_728-515


title: single neuron, striatum, F04_10007013-OGC20-sal_1_A10__N419Barcode_712-502


title: single neuron, striatum, B10_10007013-OGC20-sal_1_G07__N419Barcode_707-506


title: single neuron, striatum, F09_10007013-OGC20-sal_1_F10__N419Barcode_712-516


title: single neuron, striatum, F11_10007015-OGC22-sal_1_L20__N419Barcode_724-520


title: single neuron, striatum, G09_10007015-OGC22-sal_1_E21__N419Barcode_726-505


title: single neuron, striatum, E11_10007015-OGC22-sal_1_B20__N419Barcode_724-513


title: single neuron, striatum, D10_10007015-OGC22-sal_1_H19__N419Barcode_723-517


title: single neuron, striatum, D08_10007017-OGC17-sal_1_I24__N419Barcode_729-507


title: single neuron, striatum, E06_10007013-OGC20-sal_1_G09__N419Barcode_711-506


title: single neuron, striatum, A07_10007017-OGC17-sal_1_E22__N419Barcode_727-505


title: single neuron, striatum, G01_10007013-OGC20-sal_1_J10__N419Barcode_712-518


title: single neuron, striatum, C09_10007017-OGC17-sal_1_N23__N419Barcode_728-521


title: single neuron, striatum, A02_10007017-OGC17-sal_1_P21__N419Barcode_726-522


title: single neuron, striatum, A12_10007015-OGC22-sal_1_K17__N419Barcode_721-508


title: single neuron, striatum, D04_10007013-OGC20-sal_1_I08__N419Barcode_710-507


title: single neuron, striatum, H05_10007013-OGC20-sal_1_I11__N419Barcode_714-507


title: single neuron, striatum, A09_10007013-OGC20-sal_1_J06__N419Barcode_706-518


title: single neuron, striatum, D04_10007017-OGC17-sal_1_E24__N419Barcode_729-505


title: single neuron, striatum, E03_10007015-OGC22-sal_1_L19__N419Barcode_723-520


title: single neuron, striatum, A03_10007013-OGC20-sal_1_D06__N419Barcode_706-515


title: single neuron, striatum, B04_10007013-OGC20-sal_1_A07__N419Barcode_707-502


title: single neuron, striatum, D07_10007017-OGC17-sal_1_H24__N419Barcode_729-517


title: single neuron, striatum, C10_10007017-OGC17-sal_1_O23__N419Barcode_728-511


title: single neuron, striatum, F03_10007015-OGC22-sal_1_F20__N419Barcode_724-516


title: single neuron, striatum, A08_10007013-OGC20-sal_1_I06__N419Barcode_706-507


title: single neuron, striatum, B05_10007013-OGC20-sal_1_B07__N419Barcode_707-513


title: single neuron, striatum, D03_10007013-OGC20-sal_1_H08__N419Barcode_710-517


title: single neuron, striatum, E02_10007013-OGC20-sal_1_C09__N419Barcode_711-503


title: single neuron, striatum, D02_10007015-OGC22-sal_1_A19__N419Barcode_723-502


title: single neuron, striatum, A09_10007015-OGC22-sal_1_H17__N419Barcode_721-517


title: single neuron, striatum, B07_10007013-OGC20-sal_1_D07__N419Barcode_707-515


title: single neuron, striatum, E09_10007013-OGC20-sal_1_J09__N419Barcode_711-518


title: single neuron, striatum, D06_10007015-OGC22-sal_1_E19__N419Barcode_723-505


title: single neuron, striatum, C04_10007017-OGC17-sal_1_J23__N419Barcode_728-518


title: single neuron, striatum, D08_10007015-OGC22-sal_1_F19__N419Barcode_723-516


title: single neuron, striatum, C01_10007013-OGC20-sal_1_J07__N419Barcode_707-518


title: single neuron, striatum, B09_10007017-OGC17-sal_1_C23__N419Barcode_728-503


title: single neuron, striatum, A06_10007017-OGC17-sal_1_D22__N419Barcode_727-515

value: unknown


title: single neuron, striatum, F07_10007013-OGC20-sal_1_D10__N419Barcode_712-515


title: single neuron, striatum, H9_1000701201-OGC16-sal_1_6ul_1__IL6882-714-521


title: single neuron, striatum, H9_1000701204-OGC16-sal_1_4ul_1__IL6985-719-521

value: vClusters


title: single neuron, striatum, H9_1000700602-OGC11-sal_1_10ul_1__IL6807-723-511


title: single neuron, striatum, H9_1000701001-OGC14-sal_1_6ul_1__IL6882-718-506


title: single neuron, striatum, H9_1000700401-OGC7-coc_1_12ul_1__IL6807-714-517


title: single neuron, striatum, H8_1000701204-OGC16-sal_1_4ul_1__IL6985-718-521


title: single neuron, striatum, H8_1000700102-OGC9-sal_1_0ul_1__IL6983-718-503


title: single neuron, striatum, H8_1000700401-OGC7-coc_1_10ul_1__IL6778-723-521


title: single neuron, striatum, H7_1000701204-OGC16-sal_1_4ul_1__IL6985-716-521


title: single neuron, striatum, H7_1000701201-OGC16-sal_1_6ul_1__IL6882-712-521


title: single neuron, striatum, D01_10007015-OGC22-sal_1_P18__N419Barcode_722-522


title: single neuron, striatum, H5_1000701204-OGC16-sal_1_10ul_1__IL6985-715-521


title: single neuron, striatum, H7_1000700102-OGC9-sal_1_8ul_1__IL6983-716-503


title: single neuron, striatum, H6_1000700602-OGC11-sal_1_4ul_1__IL6807-721-511


title: single neuron, striatum, H5_1000701201-OGC16-sal_1_4ul_1__IL6882-711-521


title: single neuron, striatum, H8_1000701001-OGC14-sal_1_6ul_1__IL6882-716-506


title: single neuron, striatum, H7_1000701001-OGC14-sal_1_4ul_1__IL6882-715-506


title: single neuron, striatum, H5_1000700102-OGC9-sal_1_4ul_1__IL6983-715-503


title: single neuron, striatum, H5_1000700401-OGC7-coc_1_8ul_1__IL6807-710-517


title: single neuron, striatum, H5_1000701001-OGC14-sal_1_6ul_1__IL6882-714-506


title: single neuron, striatum, H5_1000700101-OGC9-sal_1_38ul_1__IL6778-729-503


title: single neuron, striatum, H5_1000700602-OGC11-sal_1_6ul_1__IL6807-720-511


title: single neuron, striatum, H4_1000701204-OGC16-sal_1_2ul_1__IL6985-714-521


title: single neuron, striatum, H8_1000700602-OGC11-sal_1_10ul_1__IL6807-722-511


title: single neuron, striatum, H4_1000700401-OGC7-coc_1_12ul_1__IL6778-719-521


title: single neuron, striatum, H4_1000700602-OGC11-sal_1_8ul_1__IL6807-719-511


title: single neuron, striatum, H4_1000700102-OGC9-sal_1_8ul_1__IL6983-714-503


title: single neuron, striatum, H3_1000701204-OGC16-sal_1_4ul_1__IL6985-712-521


title: single neuron, striatum, H4_1000701001-OGC14-sal_1_4ul_1__IL6882-712-506


title: single neuron, striatum, H3_1000701201-OGC16-sal_1_4ul_1__IL6882-707-521


title: single neuron, striatum, H2_1000701204-OGC16-sal_1_6ul_1__IL6985-711-521


title: single neuron, striatum, H3_1000700101-OGC9-sal_1_22ul_1__IL6778-727-503


title: single neuron, striatum, H3_1000700602-OGC11-sal_1_4ul_1__IL6807-718-511


title: single neuron, striatum, H2_1000701201-OGC16-sal_1_6ul_1__IL6882-706-521


title: single neuron, striatum, H4_1000701201-OGC16-sal_1_4ul_1__IL6882-710-521


title: single neuron, striatum, H2_1000701001-OGC14-sal_1_6ul_1__IL6882-710-506


title: single neuron, striatum, H12_1000700401-OGC7-coc_1_8ul_1__IL6807-715-517


title: single neuron, striatum, H1_1000700102-OGC9-sal_1_0ul_1__IL6983-711-503


title: single neuron, striatum, H1_1000700101-OGC9-sal_1_38ul_1__IL6778-724-503


title: single neuron, striatum, H11_1000701001-OGC14-sal_1_6ul_1__IL6882-720-506


title: single neuron, striatum, H2_1000700102-OGC9-sal_1_6ul_1__IL6983-712-503


title: single neuron, striatum, H2_1000700101-OGC9-sal_1_38ul_1__IL6778-726-503


title: single neuron, striatum, H1_1000701001-OGC14-sal_1_4ul_1__IL6882-707-506


title: single neuron, striatum, H11_1000700102-OGC9-sal_1_2ul_1__IL6983-720-503


title: single neuron, striatum, H11_1000700401-OGC7-coc_1_14ul_1__IL6778-726-521


title: single neuron, striatum, H10_1000701201-OGC16-sal_1_8ul_1__IL6882-715-521


title: single neuron, striatum, H10_1000701001-OGC14-sal_1_2ul_1__IL6882-719-506


title: single neuron, striatum, H11_1000700101-OGC9-sal_1_46ul_1__IL6778-705-515


title: single neuron, striatum, H10_1000701204-OGC16-sal_1_6ul_1__IL6985-720-521


title: single neuron, striatum, H10_1000700602-OGC11-sal_1_10ul_1__IL6807-724-511


title: single neuron, striatum, H3_1000701001-OGC14-sal_1_10ul_1__IL6882-711-506


title: single neuron, striatum, H3_1000700401-OGC7-coc_1_14ul_1__IL6778-718-521


title: single neuron, striatum, G9_1000700602-OGC11-sal_1_8ul_1__IL6807-714-511


title: single neuron, striatum, G9_1000701201-OGC16-sal_1_6ul_1__IL6882-702-521


title: single neuron, striatum, G9_1000701001-OGC14-sal_1_4ul_1__IL6882-703-506


title: single neuron, striatum, G9_1000700401-OGC7-coc_1_8ul_1__IL6778-711-521


title: single neuron, striatum, G8_1000701204-OGC16-sal_1_4ul_1__IL6985-705-521


title: single neuron, striatum, G8_1000701001-OGC14-sal_1_4ul_1__IL6882-702-506


title: single neuron, striatum, G8_1000700102-OGC9-sal_1_8ul_1__IL6983-706-503


title: single neuron, striatum, H11_1000701201-OGC16-sal_1_6ul_1__IL6882-716-521


title: single neuron, striatum, G7_1000701001-OGC14-sal_1_6ul_1__IL6882-701-506


title: single neuron, striatum, G7_1000700401-OGC7-coc_1_22ul_1__IL6807-703-517


title: single neuron, striatum, G7_1000700602-OGC11-sal_1_8ul_1__IL6807-711-511


title: single neuron, striatum, G6_1000701204-OGC16-sal_1_4ul_1__IL6985-704-521


title: single neuron, striatum, G6_1000700602-OGC11-sal_1_8ul_1__IL6807-710-511


title: single neuron, striatum, G7_1000700102-OGC9-sal_1_6ul_1__IL6983-705-503


title: single neuron, striatum, G9_1000701204-OGC16-sal_1_6ul_1__IL6985-706-521


title: single neuron, striatum, G6_1000700101-OGC9-sal_1_22ul_1__IL6807-716-513


title: single neuron, striatum, G6_1000701201-OGC16-sal_1_4ul_1__IL6882-729-510


title: single neuron, striatum, B09_10007015-OGC22-sal_1_B18__N419Barcode_722-513


title: single neuron, striatum, G6_1000700401-OGC7-coc_1_18ul_1__IL6778-706-521


title: single neuron, striatum, G9_1000700101-OGC9-sal_1_38ul_1__IL6778-720-503


title: single neuron, striatum, G6_1000701001-OGC14-sal_1_2ul_1__IL6882-729-516


title: single neuron, striatum, G5_1000701201-OGC16-sal_1_6ul_1__IL6882-728-510


title: single neuron, striatum, G5_1000701001-OGC14-sal_1_4ul_1__IL6882-728-516


title: single neuron, striatum, G5_1000701204-OGC16-sal_1_4ul_1__IL6985-703-521


title: single neuron, striatum, G5_1000700602-OGC11-sal_1_6ul_1__IL6807-707-511


title: single neuron, striatum, G5_1000700101-OGC9-sal_1_22ul_1__IL6807-715-513


title: single neuron, striatum, G4_1000701204-OGC16-sal_1_6ul_1__IL6985-702-521


title: single neuron, striatum, G4_1000701201-OGC16-sal_1_4ul_1__IL6882-727-510


title: single neuron, striatum, G8_1000701201-OGC16-sal_1_6ul_1__IL6882-701-521


title: single neuron, striatum, G4_1000701001-OGC14-sal_1_4ul_1__IL6882-727-516


title: single neuron, striatum, G8_1000700602-OGC11-sal_1_14ul_1__IL6807-712-511


title: single neuron, striatum, G4_1000700401-OGC7-coc_1_10ul_1__IL6807-702-517


title: single neuron, striatum, G4_1000700102-OGC9-sal_1_6ul_1__IL6983-703-503


title: single neuron, striatum, G3_1000701201-OGC16-sal_1_4ul_1__IL6882-726-510


title: single neuron, striatum, G3_1000701204-OGC16-sal_1_2ul_1__IL6985-701-521


title: single neuron, striatum, G3_1000701001-OGC14-sal_1_6ul_1__IL6882-726-516


title: single neuron, striatum, G3_1000700101-OGC9-sal_1_30ul_1__IL6778-714-503


title: single neuron, striatum, G3_1000700602-OGC11-sal_1_12ul_1__IL6807-705-511


title: single neuron, striatum, G3_1000700401-OGC7-coc_1_18ul_1__IL6807-701-517


title: single neuron, striatum, G2_1000701201-OGC16-sal_1_2ul_1__IL6882-724-510


title: single neuron, striatum, G2_1000700602-OGC11-sal_1_8ul_1__IL6807-704-511


title: single neuron, striatum, G5_1000700102-OGC9-sal_1_4ul_1__IL6983-704-503


title: single neuron, striatum, G2_1000700401-OGC7-coc_1_18ul_1__IL6778-703-521


title: single neuron, striatum, G1_1000701204-OGC16-sal_1_4ul_1__IL6985-728-510


title: single neuron, striatum, G2_1000700102-OGC9-sal_1_6ul_1__IL6983-702-503


title: single neuron, striatum, G1_1000700602-OGC11-sal_1_8ul_1__IL6807-703-511


title: single neuron, striatum, G4_1000700602-OGC11-sal_1_8ul_1__IL6807-706-511


title: single neuron, striatum, G1_1000700401-OGC7-coc_1_18ul_1__IL6778-702-521


title: single neuron, striatum, G1_1000701201-OGC16-sal_1_6ul_1__IL6882-723-510


title: single neuron, striatum, G1_1000700102-OGC9-sal_1_8ul_1__IL6983-701-503


title: single neuron, striatum, G12_1000701001-OGC14-sal_1_8ul_1__IL6882-706-506


title: single neuron, striatum, G12_1000700401-OGC7-coc_1_14ul_1__IL6778-715-521


title: single neuron, striatum, G1_1000700101-OGC9-sal_1_38ul_1__IL6778-712-503


title: single neuron, striatum, G11_1000701001-OGC14-sal_1_6ul_1__IL6882-705-506


title: single neuron, striatum, G11_1000701201-OGC16-sal_1_6ul_1__IL6882-704-521


title: single neuron, striatum, G11_1000701204-OGC16-sal_1_4ul_1__IL6985-707-521


title: single neuron, striatum, G11_1000700602-OGC11-sal_1_14ul_1__IL6807-716-511


title: single neuron, striatum, G11_1000700101-OGC9-sal_1_46ul_1__IL6778-722-503


title: single neuron, striatum, G10_1000701201-OGC16-sal_1_2ul_1__IL6882-703-521


title: single neuron, striatum, G10_1000701001-OGC14-sal_1_6ul_1__IL6882-704-506


title: single neuron, striatum, G2_1000701204-OGC16-sal_1_4ul_1__IL6985-729-510


title: single neuron, striatum, G10_1000700401-OGC7-coc_1_14ul_1__IL6807-705-517


title: single neuron, striatum, G10_1000700102-OGC9-sal_1_4ul_1__IL6983-707-503


title: single neuron, striatum, G10_1000700602-OGC11-sal_1_14ul_1__IL6807-715-511


title: single neuron, striatum, G1_1000701001-OGC14-sal_1_4ul_1__IL6882-724-516


title: single neuron, striatum, G10_1000700101-OGC9-sal_1_30ul_1__IL6778-721-503


title: single neuron, striatum, G12_1000701204-OGC16-sal_1_4ul_1__IL6985-710-521


title: single neuron, striatum, F9_1000700602-OGC11-sal_1_10ul_1__IL6807-728-521


title: single neuron, striatum, F9_1000700101-OGC9-sal_1_46ul_1__IL6778-706-503


title: single neuron, striatum, F9_1000701204-OGC16-sal_1_6ul_1__IL6985-723-510


title: single neuron, striatum, F9_1000701201-OGC16-sal_1_6ul_1__IL6882-720-510


title: single neuron, striatum, F9_1000700401-OGC7-coc_1_22ul_1__IL6778-727-510


title: single neuron, striatum, F7_1000701001-OGC14-sal_1_4ul_1__IL6882-719-516


title: single neuron, striatum, F7_1000700102-OGC9-sal_1_4ul_1__IL6983-726-513


title: single neuron, striatum, F8_1000700401-OGC7-coc_1_18ul_1__IL6807-729-506


title: single neuron, striatum, F9_1000701001-OGC14-sal_1_6ul_1__IL6882-720-516


title: single neuron, striatum, F8_1000700101-OGC9-sal_1_54ul_1__IL6778-705-503


title: single neuron, striatum, F7_1000701201-OGC16-sal_1_4ul_1__IL6882-718-510


title: single neuron, striatum, F7_1000700602-OGC11-sal_1_8ul_1__IL6807-726-521


title: single neuron, striatum, F6_1000701204-OGC16-sal_1_4ul_1__IL6985-721-510


title: single neuron, striatum, F8_1000700102-OGC9-sal_1_8ul_1__IL6983-727-513


title: single neuron, striatum, F6_1000701201-OGC16-sal_1_4ul_1__IL6882-716-510


title: single neuron, striatum, F6_1000700401-OGC7-coc_1_14ul_1__IL6778-723-510


title: single neuron, striatum, F6_1000701001-OGC14-sal_1_4ul_1__IL6882-718-516


title: single neuron, striatum, F7_1000700101-OGC9-sal_1_30ul_1__IL6807-711-513


title: single neuron, striatum, F5_1000700602-OGC11-sal_1_6ul_1__IL6807-723-521


title: single neuron, striatum, F5_1000701001-OGC14-sal_1_6ul_1__IL6882-716-516


title: single neuron, striatum, F5_1000700401-OGC7-coc_1_18ul_1__IL6778-722-510


title: single neuron, striatum, F5_1000701201-OGC16-sal_1_6ul_1__IL6882-715-510


title: single neuron, striatum, F5_1000700102-OGC9-sal_1_10ul_1__IL6983-724-513


title: single neuron, striatum, F5_1000700101-OGC9-sal_1_38ul_1__IL6807-707-513


title: single neuron, striatum, F8_1000701204-OGC16-sal_1_4ul_1__IL6985-722-510


title: single neuron, striatum, F4_1000701204-OGC16-sal_1_6ul_1__IL6985-720-510


title: single neuron, striatum, F4_1000700602-OGC11-sal_1_8ul_1__IL6807-722-521


title: single neuron, striatum, F4_1000701001-OGC14-sal_1_4ul_1__IL6882-715-516


title: single neuron, striatum, F4_1000701201-OGC16-sal_1_4ul_1__IL6882-714-510


title: single neuron, striatum, F4_1000700401-OGC7-coc_1_18ul_1__IL6778-721-510


title: single neuron, striatum, F4_1000700102-OGC9-sal_1_4ul_1__IL6983-723-513


title: single neuron, striatum, F1_1000701201-OGC16-sal_1_6ul_1__IL6882-710-510


title: single neuron, striatum, F3_1000700401-OGC7-coc_1_18ul_1__IL6807-727-506


title: single neuron, striatum, F3_1000701204-OGC16-sal_1_6ul_1__IL6985-719-510


title: single neuron, striatum, F2_1000700602-OGC11-sal_1_4ul_1__IL6807-720-521


title: single neuron, striatum, F2_1000701001-OGC14-sal_1_6ul_1__IL6882-712-516


title: single neuron, striatum, F2_1000700101-OGC9-sal_1_30ul_1__IL6778-729-513


title: single neuron, striatum, F2_1000701201-OGC16-sal_1_4ul_1__IL6882-711-510


title: single neuron, striatum, F2_1000700401-OGC7-coc_1_18ul_1__IL6778-719-510


title: single neuron, striatum, F2_1000700102-OGC9-sal_1_6ul_1__IL6983-722-513


title: single neuron, striatum, F3_1000701001-OGC14-sal_1_2ul_1__IL6882-714-516


title: single neuron, striatum, F2_1000701204-OGC16-sal_1_2ul_1__IL6985-718-510


title: single neuron, striatum, F1_1000701001-OGC14-sal_1_4ul_1__IL6882-711-516


title: single neuron, striatum, F12_1000701204-OGC16-sal_1_4ul_1__IL6985-727-510


title: single neuron, striatum, F1_1000700401-OGC7-coc_1_12ul_1__IL6778-718-510


title: single neuron, striatum, F12_1000701001-OGC14-sal_1_6ul_1__IL6882-723-516


title: single neuron, striatum, F12_1000700602-OGC11-sal_1_8ul_1__IL6807-702-511


title: single neuron, striatum, F12_1000700401-OGC7-coc_1_22ul_1__IL6778-701-521


title: single neuron, striatum, F11_1000701204-OGC16-sal_1_6ul_1__IL6985-726-510


title: single neuron, striatum, F11_1000701201-OGC16-sal_1_8ul_1__IL6882-722-510


title: single neuron, striatum, F12_1000700101-OGC9-sal_1_30ul_1__IL6778-711-503


title: single neuron, striatum, F11_1000700401-OGC7-coc_1_22ul_1__IL6778-729-510


title: single neuron, striatum, F11_1000701001-OGC14-sal_1_4ul_1__IL6882-722-516


title: single neuron, striatum, F10_1000701001-OGC14-sal_1_2ul_1__IL6882-721-516


title: single neuron, striatum, F11_1000700101-OGC9-sal_1_38ul_1__IL6778-710-503


title: single neuron, striatum, F10_1000701204-OGC16-sal_1_4ul_1__IL6985-724-510


title: single neuron, striatum, F3_1000701201-OGC16-sal_1_2ul_1__IL6882-712-510


title: single neuron, striatum, F10_1000700401-OGC7-coc_1_12ul_1__IL6778-728-510


title: single neuron, striatum, F10_1000700102-OGC9-sal_1_8ul_1__IL6983-728-513


title: single neuron, striatum, E9_1000701204-OGC16-sal_1_4ul_1__IL6985-711-510


title: single neuron, striatum, E9_1000700101-OGC9-sal_1_30ul_1__IL6778-724-513


title: single neuron, striatum, E8_1000701201-OGC16-sal_1_4ul_1__IL6882-703-510


title: single neuron, striatum, E7_1000701204-OGC16-sal_1_0ul_1__IL6985-707-510


title: single neuron, striatum, E8_1000700401-OGC7-coc_1_14ul_1__IL6807-723-506


title: single neuron, striatum, E8_1000700102-OGC9-sal_1_4ul_1__IL6983-718-513


title: single neuron, striatum, E9_1000700401-OGC7-coc_1_14ul_1__IL6778-712-510


title: single neuron, striatum, E7_1000700602-OGC11-sal_1_8ul_1__IL6807-715-521


title: single neuron, striatum, E9_1000700602-OGC11-sal_1_8ul_1__IL6807-716-521


title: single neuron, striatum, E9_1000701001-OGC14-sal_1_8ul_1__IL6882-705-516


title: single neuron, striatum, E7_1000701201-OGC16-sal_1_6ul_1__IL6882-702-510


title: single neuron, striatum, E7_1000700401-OGC7-coc_1_18ul_1__IL6807-722-506


title: single neuron, striatum, E7_1000701001-OGC14-sal_1_4ul_1__IL6882-704-516


title: single neuron, striatum, E7_1000700102-OGC9-sal_1_4ul_1__IL6983-716-513


title: single neuron, striatum, F10_1000701201-OGC16-sal_1_6ul_1__IL6882-721-510


title: single neuron, striatum, E6_1000700401-OGC7-coc_1_22ul_1__IL6778-707-510


title: single neuron, striatum, E5_1000701201-OGC16-sal_1_6ul_1__IL6882-729-520


title: single neuron, striatum, E6_1000700602-OGC11-sal_1_10ul_1__IL6807-714-521


title: single neuron, striatum, E6_1000701001-OGC14-sal_1_2ul_1__IL6882-703-516


title: single neuron, striatum, E5_1000701001-OGC14-sal_1_2ul_1__IL6882-702-516


title: single neuron, striatum, E5_1000701204-OGC16-sal_1_4ul_1__IL6985-705-510


title: single neuron, striatum, E5_1000700602-OGC11-sal_1_8ul_1__IL6807-712-521


title: single neuron, striatum, E5_1000700401-OGC7-coc_1_30ul_1__IL6807-721-506


title: single neuron, striatum, E5_1000700102-OGC9-sal_1_8ul_1__IL6983-715-513


title: single neuron, striatum, E9_1000701201-OGC16-sal_1_6ul_1__IL6882-704-510


title: single neuron, striatum, E8_1000700101-OGC9-sal_1_30ul_1__IL6807-703-513


title: single neuron, striatum, E8_1000701204-OGC16-sal_1_4ul_1__IL6985-710-510


title: single neuron, striatum, E4_1000701204-OGC16-sal_1_2ul_1__IL6985-704-510


title: single neuron, striatum, E4_1000701001-OGC14-sal_1_6ul_1__IL6882-701-516


title: single neuron, striatum, E7_1000700101-OGC9-sal_1_38ul_1__IL6807-702-513


title: single neuron, striatum, E6_1000701204-OGC16-sal_1_6ul_1__IL6985-706-510


title: single neuron, striatum, E6_1000701201-OGC16-sal_1_6ul_1__IL6882-701-510


title: single neuron, striatum, E4_1000700102-OGC9-sal_1_4ul_1__IL6983-714-513


title: single neuron, striatum, E3_1000700401-OGC7-coc_1_22ul_1__IL6778-704-510


title: single neuron, striatum, E2_1000701001-OGC14-sal_1_6ul_1__IL6882-729-505


title: single neuron, striatum, E4_1000700401-OGC7-coc_1_10ul_1__IL6778-705-510


title: single neuron, striatum, E3_1000701201-OGC16-sal_1_6ul_1__IL6882-727-520


title: single neuron, striatum, E2_1000701204-OGC16-sal_1_2ul_1__IL6985-702-510


title: single neuron, striatum, E2_1000700401-OGC7-coc_1_18ul_1__IL6778-703-510


title: single neuron, striatum, E2_1000700102-OGC9-sal_1_4ul_1__IL6983-712-513


title: single neuron, striatum, E1_1000700401-OGC7-coc_1_12ul_1__IL6807-720-506


title: single neuron, striatum, E12_1000701201-OGC16-sal_1_4ul_1__IL6882-707-510


title: single neuron, striatum, E1_1000701001-OGC14-sal_1_8ul_1__IL6882-728-505


title: single neuron, striatum, E1_1000701201-OGC16-sal_1_4ul_1__IL6882-724-520


title: single neuron, striatum, E12_1000701204-OGC16-sal_1_6ul_1__IL6985-715-510


title: single neuron, striatum, E3_1000700602-OGC11-sal_1_2ul_1__IL6807-710-521


title: single neuron, striatum, E2_1000700602-OGC11-sal_1_12ul_1__IL6807-707-521


title: single neuron, striatum, E1_1000700101-OGC9-sal_1_38ul_1__IL6778-719-513


title: single neuron, striatum, E12_1000701001-OGC14-sal_1_8ul_1__IL6882-710-516


title: single neuron, striatum, E12_1000700602-OGC11-sal_1_18ul_1__IL6807-719-521


title: single neuron, striatum, E11_1000701201-OGC16-sal_1_4ul_1__IL6882-706-510


title: single neuron, striatum, E11_1000701204-OGC16-sal_1_2ul_1__IL6985-714-510


title: single neuron, striatum, E3_1000701204-OGC16-sal_1_2ul_1__IL6985-703-510


title: single neuron, striatum, E4_1000700602-OGC11-sal_1_10ul_1__IL6807-711-521


title: single neuron, striatum, E11_1000701001-OGC14-sal_1_2ul_1__IL6882-707-516


title: single neuron, striatum, E4_1000701201-OGC16-sal_1_4ul_1__IL6882-728-520


title: single neuron, striatum, E2_1000701201-OGC16-sal_1_2ul_1__IL6882-726-520


title: single neuron, striatum, E10_1000701201-OGC16-sal_1_4ul_1__IL6882-705-510


title: single neuron, striatum, E10_1000701204-OGC16-sal_1_2ul_1__IL6985-712-510


title: single neuron, striatum, E11_1000700102-OGC9-sal_1_8ul_1__IL6983-720-513


title: single neuron, striatum, E11_1000700101-OGC9-sal_1_46ul_1__IL6807-704-513


title: single neuron, striatum, E10_1000701001-OGC14-sal_1_4ul_1__IL6882-706-516


title: single neuron, striatum, E10_1000700101-OGC9-sal_1_30ul_1__IL6778-726-513


title: single neuron, striatum, E10_1000700401-OGC7-coc_1_18ul_1__IL6807-724-506


title: single neuron, striatum, D9_1000701204-OGC16-sal_1_8ul_1__IL6985-726-520


title: single neuron, striatum, E10_1000700602-OGC11-sal_1_8ul_1__IL6807-718-521


title: single neuron, striatum, D9_1000701201-OGC16-sal_1_4ul_1__IL6882-720-520


title: single neuron, striatum, D9_1000701001-OGC14-sal_1_6ul_1__IL6882-723-505


title: single neuron, striatum, D8_1000700101-OGC9-sal_1_30ul_1__IL6778-715-513


title: single neuron, striatum, D8_1000700602-OGC11-sal_1_4ul_1__IL6807-702-521


title: single neuron, striatum, D8_1000701201-OGC16-sal_1_6ul_1__IL6882-719-520


title: single neuron, striatum, D8_1000701204-OGC16-sal_1_2ul_1__IL6985-724-520


title: single neuron, striatum, D8_1000700102-OGC9-sal_1_6ul_1__IL6983-706-513


title: single neuron, striatum, D9_1000700401-OGC7-coc_1_22ul_1__IL6778-727-520


title: single neuron, striatum, D8_1000700401-OGC7-coc_1_8ul_1__IL6807-716-506


title: single neuron, striatum, D7_1000701204-OGC16-sal_1_0ul_1__IL6985-723-520


title: single neuron, striatum, E11_1000700401-OGC7-coc_1_18ul_1__IL6778-715-510


title: single neuron, striatum, D7_1000701201-OGC16-sal_1_8ul_1__IL6882-718-520


title: single neuron, striatum, D7_1000701001-OGC14-sal_1_4ul_1__IL6882-721-505


title: single neuron, striatum, D7_1000700401-OGC7-coc_1_14ul_1__IL6778-724-520


title: single neuron, striatum, D7_1000700101-OGC9-sal_1_30ul_1__IL6807-726-502


title: single neuron, striatum, D7_1000700102-OGC9-sal_1_6ul_1__IL6983-705-513


title: single neuron, striatum, D6_1000701204-OGC16-sal_1_4ul_1__IL6985-722-520


title: single neuron, striatum, D6_1000700602-OGC11-sal_1_6ul_1__IL6807-729-510


title: single neuron, striatum, D6_1000701001-OGC14-sal_1_2ul_1__IL6882-720-505


title: single neuron, striatum, D6_1000701201-OGC16-sal_1_6ul_1__IL6882-716-520


title: single neuron, striatum, D6_1000700401-OGC7-coc_1_14ul_1__IL6778-723-520


title: single neuron, striatum, D5_1000701201-OGC16-sal_1_6ul_1__IL6882-715-520


title: single neuron, striatum, D5_1000700401-OGC7-coc_1_18ul_1__IL6778-722-520


title: single neuron, striatum, D5_1000700602-OGC11-sal_1_12ul_1__IL6807-728-510


title: single neuron, striatum, D8_1000701001-OGC14-sal_1_6ul_1__IL6882-722-505


title: single neuron, striatum, D4_1000701204-OGC16-sal_1_2ul_1__IL6985-721-520


title: single neuron, striatum, D5_1000700102-OGC9-sal_1_6ul_1__IL6983-704-513


title: single neuron, striatum, D4_1000700602-OGC11-sal_1_8ul_1__IL6807-727-510


title: single neuron, striatum, D4_1000701201-OGC16-sal_1_6ul_1__IL6882-714-520


title: single neuron, striatum, D4_1000700401-OGC7-coc_1_10ul_1__IL6807-715-506


title: single neuron, striatum, D3_1000701204-OGC16-sal_1_2ul_1__IL6985-720-520


title: single neuron, striatum, D3_1000701001-OGC14-sal_1_6ul_1__IL6882-718-505


title: single neuron, striatum, D2_1000700401-OGC7-coc_1_10ul_1__IL6807-714-506


title: single neuron, striatum, D2_1000701001-OGC14-sal_1_6ul_1__IL6882-716-505


title: single neuron, striatum, D3_1000700602-OGC11-sal_1_6ul_1__IL6807-726-510


title: single neuron, striatum, D2_1000701201-OGC16-sal_1_6ul_1__IL6882-711-520


title: single neuron, striatum, D2_1000701204-OGC16-sal_1_2ul_1__IL6985-719-520


title: single neuron, striatum, D3_1000700401-OGC7-coc_1_12ul_1__IL6778-720-520


title: single neuron, striatum, D3_1000700101-OGC9-sal_1_22ul_1__IL6807-723-502


title: single neuron, striatum, D2_1000700102-OGC9-sal_1_6ul_1__IL6983-702-513


title: single neuron, striatum, D3_1000701201-OGC16-sal_1_6ul_1__IL6882-712-520


title: single neuron, striatum, D5_1000701001-OGC14-sal_1_6ul_1__IL6882-719-505


title: single neuron, striatum, D2_1000700101-OGC9-sal_1_30ul_1__IL6778-710-513


title: single neuron, striatum, D1_1000700102-OGC9-sal_1_6ul_1__IL6983-701-513


title: single neuron, striatum, D2_1000700602-OGC11-sal_1_10ul_1__IL6807-724-510


title: single neuron, striatum, D1_1000700401-OGC7-coc_1_22ul_1__IL6778-718-520


title: single neuron, striatum, D1_1000700101-OGC9-sal_1_30ul_1__IL6778-707-513


title: single neuron, striatum, D12_1000701001-OGC14-sal_1_2ul_1__IL6882-727-505


title: single neuron, striatum, D12_1000701201-OGC16-sal_1_4ul_1__IL6882-723-520


title: single neuron, striatum, D12_1000701204-OGC16-sal_1_4ul_1__IL6985-729-520


title: single neuron, striatum, D12_1000700602-OGC11-sal_1_30ul_1__IL6807-705-521


title: single neuron, striatum, D11_1000701204-OGC16-sal_1_4ul_1__IL6985-728-520


title: single neuron, striatum, D11_1000700602-OGC11-sal_1_6ul_1__IL6807-704-521


title: single neuron, striatum, D11_1000701001-OGC14-sal_1_6ul_1__IL6882-726-505


title: single neuron, striatum, D11_1000701201-OGC16-sal_1_6ul_1__IL6882-722-520


title: single neuron, striatum, D11_1000700401-OGC7-coc_1_18ul_1__IL6807-718-506


title: single neuron, striatum, D10_1000700602-OGC11-sal_1_18ul_1__IL6807-703-521


title: single neuron, striatum, D10_1000701201-OGC16-sal_1_4ul_1__IL6882-721-520


title: single neuron, striatum, D10_1000701001-OGC14-sal_1_4ul_1__IL6882-724-505


title: single neuron, striatum, D10_1000701204-OGC16-sal_1_6ul_1__IL6985-727-520


title: single neuron, striatum, D10_1000700401-OGC7-coc_1_12ul_1__IL6778-728-520


title: single neuron, striatum, C9_1000700101-OGC9-sal_1_30ul_1__IL6807-719-502


title: single neuron, striatum, C9_1000701204-OGC16-sal_1_4ul_1__IL6985-714-520


title: single neuron, striatum, D10_1000700102-OGC9-sal_1_6ul_1__IL6983-707-513


title: single neuron, striatum, C9_1000700401-OGC7-coc_1_12ul_1__IL6778-712-520


title: single neuron, striatum, C8_1000701204-OGC16-sal_1_4ul_1__IL6985-712-520


title: single neuron, striatum, C7_1000701204-OGC16-sal_1_2ul_1__IL6985-711-520


title: single neuron, striatum, C7_1000700102-OGC9-sal_1_4ul_1__IL6983-726-502


title: single neuron, striatum, C8_1000700602-OGC11-sal_1_10ul_1__IL6807-718-510


title: single neuron, striatum, C9_1000700602-OGC11-sal_1_12ul_1__IL6807-719-510


title: single neuron, striatum, C9_1000701001-OGC14-sal_1_2ul_1__IL6882-711-505


title: single neuron, striatum, C8_1000700101-OGC9-sal_1_38ul_1__IL6778-702-513


title: single neuron, striatum, C8_1000701201-OGC16-sal_1_6ul_1__IL6882-704-520


title: single neuron, striatum, C7_1000700401-OGC7-coc_1_18ul_1__IL6778-710-520


title: single neuron, striatum, C6_1000700602-OGC11-sal_1_18ul_1__IL6807-715-510


title: single neuron, striatum, C7_1000701201-OGC16-sal_1_6ul_1__IL6882-703-520


title: single neuron, striatum, C6_1000701201-OGC16-sal_1_4ul_1__IL6882-702-520


title: single neuron, striatum, C8_1000700401-OGC7-coc_1_22ul_1__IL6778-711-520


title: single neuron, striatum, C7_1000701001-OGC14-sal_1_4ul_1__IL6882-707-505


title: single neuron, striatum, C9_1000701201-OGC16-sal_1_4ul_1__IL6882-705-520


title: single neuron, striatum, C6_1000701001-OGC14-sal_1_2ul_1__IL6882-706-505


title: single neuron, striatum, C8_1000701001-OGC14-sal_1_4ul_1__IL6882-710-505


title: single neuron, striatum, C6_1000700101-OGC9-sal_1_22ul_1__IL6807-716-502


title: single neuron, striatum, C5_1000701204-OGC16-sal_1_2ul_1__IL6985-707-520


title: single neuron, striatum, C5_1000700401-OGC7-coc_1_14ul_1__IL6778-706-520


title: single neuron, striatum, C5_1000701001-OGC14-sal_1_8ul_1__IL6882-705-505


title: single neuron, striatum, C7_1000700602-OGC11-sal_1_8ul_1__IL6807-716-510


title: single neuron, striatum, C5_1000701201-OGC16-sal_1_8ul_1__IL6882-701-520


title: single neuron, striatum, C5_1000700602-OGC11-sal_1_4ul_1__IL6807-714-510


title: single neuron, striatum, C6_1000701204-OGC16-sal_1_4ul_1__IL6985-710-520


title: single neuron, striatum, C5_1000700101-OGC9-sal_1_18ul_1__IL6778-728-502


title: single neuron, striatum, C4_1000701201-OGC16-sal_1_4ul_1__IL6882-729-508


title: single neuron, striatum, C4_1000700602-OGC11-sal_1_4ul_1__IL6807-712-510


title: single neuron, striatum, C4_1000701001-OGC14-sal_1_4ul_1__IL6882-704-505


title: single neuron, striatum, C6_1000700401-OGC7-coc_1_18ul_1__IL6807-707-506


title: single neuron, striatum, C4_1000700401-OGC7-coc_1_12ul_1__IL6778-705-520


title: single neuron, striatum, C4_1000700102-OGC9-sal_1_4ul_1__IL6983-723-502


title: single neuron, striatum, C3_1000700602-OGC11-sal_1_14ul_1__IL6807-711-510


title: single neuron, striatum, C3_1000701001-OGC14-sal_1_4ul_1__IL6882-703-505


title: single neuron, striatum, C2_1000701201-OGC16-sal_1_0ul_1__IL6882-727-508


title: single neuron, striatum, C2_1000701204-OGC16-sal_1_2ul_1__IL6985-704-520


title: single neuron, striatum, C3_1000701204-OGC16-sal_1_4ul_1__IL6985-705-520


title: single neuron, striatum, C2_1000700101-OGC9-sal_1_38ul_1__IL6778-724-502


title: single neuron, striatum, C2_1000700401-OGC7-coc_1_14ul_1__IL6778-703-520


title: single neuron, striatum, C3_1000701201-OGC16-sal_1_4ul_1__IL6882-728-508


title: single neuron, striatum, C2_1000701001-OGC14-sal_1_8ul_1__IL6882-702-505


title: single neuron, striatum, C1_1000701001-OGC14-sal_1_6ul_1__IL6882-701-505


title: single neuron, striatum, C4_1000701204-OGC16-sal_1_4ul_1__IL6985-706-520


title: single neuron, striatum, C3_1000700401-OGC7-coc_1_10ul_1__IL6807-706-506


title: single neuron, striatum, C12_1000701001-OGC14-sal_1_6ul_1__IL6882-715-505


title: single neuron, striatum, C12_1000701201-OGC16-sal_1_4ul_1__IL6882-710-520


title: single neuron, striatum, C12_1000701204-OGC16-sal_1_4ul_1__IL6985-718-520


title: single neuron, striatum, C1_1000700101-OGC9-sal_1_46ul_1__IL6778-723-502


title: single neuron, striatum, C11_1000701201-OGC16-sal_1_4ul_1__IL6882-707-520


title: single neuron, striatum, C12_1000700602-OGC11-sal_1_18ul_1__IL6807-722-510


title: single neuron, striatum, C12_1000700401-OGC7-coc_1_6ul_1__IL6807-712-506


title: single neuron, striatum, C11_1000701204-OGC16-sal_1_4ul_1__IL6985-716-520


title: single neuron, striatum, C11_1000700602-OGC11-sal_1_10ul_1__IL6807-721-510


title: single neuron, striatum, C11_1000701001-OGC14-sal_1_2ul_1__IL6882-714-505


title: single neuron, striatum, C1_1000701204-OGC16-sal_1_6ul_1__IL6985-703-520


title: single neuron, striatum, C11_1000700401-OGC7-coc_1_18ul_1__IL6807-711-506


title: single neuron, striatum, C3_1000700101-OGC9-sal_1_22ul_1__IL6778-726-502


title: single neuron, striatum, C10_1000701204-OGC16-sal_1_4ul_1__IL6985-715-520


title: single neuron, striatum, C10_1000701001-OGC14-sal_1_6ul_1__IL6882-712-505


title: single neuron, striatum, C10_1000700102-OGC9-sal_1_4ul_1__IL6983-728-502


title: single neuron, striatum, C10_1000700602-OGC11-sal_1_22ul_1__IL6807-720-510


title: single neuron, striatum, B9_1000701204-OGC16-sal_1_6ul_1__IL6985-729-508


title: single neuron, striatum, B9_1000701001-OGC14-sal_1_4ul_1__IL6882-726-515


title: single neuron, striatum, C10_1000700101-OGC9-sal_1_22ul_1__IL6807-720-502


title: single neuron, striatum, B9_1000700401-OGC7-coc_1_14ul_1__IL6778-727-508


title: single neuron, striatum, B9_1000700101-OGC9-sal_1_30ul_1__IL6807-712-502


title: single neuron, striatum, B8_1000701204-OGC16-sal_1_4ul_1__IL6985-728-508


title: single neuron, striatum, B8_1000701201-OGC16-sal_1_6ul_1__IL6882-721-508


title: single neuron, striatum, C1_1000700401-OGC7-coc_1_30ul_1__IL6778-702-520


title: single neuron, striatum, B8_1000701001-OGC14-sal_1_6ul_1__IL6882-724-515


title: single neuron, striatum, B8_1000700401-OGC7-coc_1_30ul_1__IL6778-726-508


title: single neuron, striatum, B8_1000700102-OGC9-sal_1_8ul_1__IL6983-718-502


title: single neuron, striatum, B7_1000701204-OGC16-sal_1_2ul_1__IL6985-727-508


title: single neuron, striatum, B7_1000700401-OGC7-coc_1_8ul_1__IL6807-704-506


title: single neuron, striatum, B6_1000700401-OGC7-coc_1_12ul_1__IL6778-723-508


title: single neuron, striatum, B7_1000700602-OGC11-sal_1_10ul_1__IL6807-701-510


title: single neuron, striatum, B7_1000700102-OGC9-sal_1_4ul_1__IL6983-716-502


title: single neuron, striatum, B5_1000701204-OGC16-sal_1_2ul_1__IL6985-724-508


title: single neuron, striatum, B5_1000701201-OGC16-sal_1_6ul_1__IL6882-718-508


title: single neuron, striatum, B5_1000700401-OGC7-coc_1_18ul_1__IL6778-722-508


title: single neuron, striatum, B5_1000701001-OGC14-sal_1_4ul_1__IL6882-721-515


title: single neuron, striatum, B5_1000700102-OGC9-sal_1_6ul_1__IL6983-715-502


title: single neuron, striatum, B3_1000701204-OGC16-sal_1_4ul_1__IL6985-722-508


title: single neuron, striatum, B4_1000700401-OGC7-coc_1_14ul_1__IL6778-721-508


title: single neuron, striatum, B4_1000700102-OGC9-sal_1_4ul_1__IL6983-714-502


title: single neuron, striatum, B4_1000701201-OGC16-sal_1_2ul_1__IL6882-716-508


title: single neuron, striatum, B4_1000701204-OGC16-sal_1_4ul_1__IL6985-723-508


title: single neuron, striatum, B4_1000701001-OGC14-sal_1_4ul_1__IL6882-720-515


title: single neuron, striatum, B3_1000701201-OGC16-sal_1_6ul_1__IL6882-715-508


title: single neuron, striatum, B8_1000700101-OGC9-sal_1_30ul_1__IL6778-720-502


title: single neuron, striatum, B3_1000700602-OGC11-sal_1_2ul_1__IL6807-728-520


title: single neuron, striatum, B2_1000701204-OGC16-sal_1_4ul_1__IL6985-721-508


title: single neuron, striatum, B3_1000700401-OGC7-coc_1_12ul_1__IL6807-703-506


title: single neuron, striatum, B3_1000701001-OGC14-sal_1_2ul_1__IL6882-719-515


title: single neuron, striatum, B6_1000701001-OGC14-sal_1_2ul_1__IL6882-722-515


title: single neuron, striatum, B7_1000701001-OGC14-sal_1_2ul_1__IL6882-723-515


title: single neuron, striatum, B6_1000701201-OGC16-sal_1_8ul_1__IL6882-719-508


title: single neuron, striatum, B7_1000701201-OGC16-sal_1_4ul_1__IL6882-720-508


title: single neuron, striatum, B6_1000701204-OGC16-sal_1_4ul_1__IL6985-726-508


title: single neuron, striatum, B2_1000700101-OGC9-sal_1_30ul_1__IL6778-714-502


title: single neuron, striatum, B2_1000701201-OGC16-sal_1_6ul_1__IL6882-714-508


title: single neuron, striatum, B1_1000701001-OGC14-sal_1_6ul_1__IL6882-716-515


title: single neuron, striatum, B9_1000701201-OGC16-sal_1_6ul_1__IL6882-722-508


title: single neuron, striatum, B2_1000700102-OGC9-sal_1_2ul_1__IL6983-712-502


title: single neuron, striatum, B1_1000700101-OGC9-sal_1_18ul_1__IL6778-712-502


title: single neuron, striatum, B1_1000701204-OGC16-sal_1_6ul_1__IL6985-720-508


title: single neuron, striatum, B12_1000701001-OGC14-sal_1_4ul_1__IL6882-729-515


title: single neuron, striatum, B12_1000700602-OGC11-sal_1_6ul_1__IL6807-706-510


title: single neuron, striatum, B11_1000701204-OGC16-sal_1_4ul_1__IL6985-702-520


title: single neuron, striatum, B1_1000700602-OGC11-sal_1_6ul_1__IL6807-726-520


title: single neuron, striatum, B10_1000701204-OGC16-sal_1_4ul_1__IL6985-701-520


title: single neuron, striatum, B10_1000701201-OGC16-sal_1_4ul_1__IL6882-723-508


title: single neuron, striatum, B1_1000700401-OGC7-coc_1_14ul_1__IL6778-718-508


title: single neuron, striatum, B1_1000701201-OGC16-sal_1_2ul_1__IL6882-712-508


title: single neuron, striatum, B12_1000700401-OGC7-coc_1_14ul_1__IL6778-701-520


title: single neuron, striatum, B12_1000700101-OGC9-sal_1_46ul_1__IL6807-714-502


title: single neuron, striatum, B2_1000701001-OGC14-sal_1_2ul_1__IL6882-718-515


title: single neuron, striatum, B2_1000700602-OGC11-sal_1_10ul_1__IL6807-727-520


title: single neuron, striatum, B11_1000701201-OGC16-sal_1_2ul_1__IL6882-724-508


title: single neuron, striatum, B11_1000701001-OGC14-sal_1_6ul_1__IL6882-728-515


title: single neuron, striatum, B11_1000700401-OGC7-coc_1_30ul_1__IL6778-729-508


title: single neuron, striatum, B10_1000701001-OGC14-sal_1_6ul_1__IL6882-727-515


title: single neuron, striatum, A9_1000700602-OGC11-sal_1_18ul_1__IL6807-721-520


title: single neuron, striatum, B2_1000700401-OGC7-coc_1_12ul_1__IL6778-719-508


title: single neuron, striatum, A8_1000701204-OGC16-sal_1_4ul_1__IL6985-715-508


title: single neuron, striatum, B10_1000700602-OGC11-sal_1_10ul_1__IL6807-704-510


title: single neuron, striatum, A8_1000700102-OGC9-sal_1_8ul_1__IL6983-706-502


title: single neuron, striatum, A7_1000700102-OGC9-sal_1_8ul_1__IL6983-705-502


title: single neuron, striatum, B10_1000700401-OGC7-coc_1_6ul_1__IL6807-705-506


title: single neuron, striatum, B10_1000700102-OGC9-sal_1_8ul_1__IL6983-719-502


title: single neuron, striatum, A9_1000701201-OGC16-sal_1_8ul_1__IL6882-706-508


title: single neuron, striatum, B12_1000701201-OGC16-sal_1_2ul_1__IL6882-726-508


title: single neuron, striatum, A5_1000701001-OGC14-sal_1_4ul_1__IL6882-710-515


title: single neuron, striatum, C1_1000700602-OGC11-sal_1_10ul_1__IL6807-707-510


title: single neuron, striatum, A9_1000701001-OGC14-sal_1_8ul_1__IL6882-712-515


title: single neuron, striatum, A7_1000701204-OGC16-sal_1_2ul_1__IL6985-714-508


title: single neuron, striatum, B11_1000700602-OGC11-sal_1_2ul_1__IL6807-705-510

value: ICj


title: single neuron, striatum, A8_1000701201-OGC16-sal_1_6ul_1__IL6882-705-508


title: single neuron, striatum, A7_1000701201-OGC16-sal_1_6ul_1__IL6882-704-508


title: single neuron, striatum, A5_1000700102-OGC9-sal_1_6ul_1__IL6983-704-502


title: single neuron, striatum, A4_1000700602-OGC11-sal_1_8ul_1__IL6807-716-520


title: single neuron, striatum, A6_1000701204-OGC16-sal_1_6ul_1__IL6985-712-508


title: single neuron, striatum, A6_1000701201-OGC16-sal_1_2ul_1__IL6882-703-508


title: single neuron, striatum, A6_1000701001-OGC14-sal_1_4ul_1__IL6882-711-515


title: single neuron, striatum, A6_1000700602-OGC11-sal_1_10ul_1__IL6807-719-520


title: single neuron, striatum, A5_1000701204-OGC16-sal_1_0ul_1__IL6985-711-508


title: single neuron, striatum, A5_1000701201-OGC16-sal_1_4ul_1__IL6882-702-508


title: single neuron, striatum, A5_1000700602-OGC11-sal_1_8ul_1__IL6807-718-520


title: single neuron, striatum, A4_1000701204-OGC16-sal_1_6ul_1__IL6985-710-508


title: single neuron, striatum, A1_1000700102-OGC9-sal_1_6ul_1__IL6983-701-502


title: single neuron, striatum, A12_1000701201-OGC16-sal_1_6ul_1__IL6882-711-508


title: single neuron, striatum, A12_1000700401-OGC7-coc_1_14ul_1__IL6778-716-508


title: single neuron, striatum, A11_1000701204-OGC16-sal_1_6ul_1__IL6985-718-508


title: single neuron, striatum, A3_1000700602-OGC11-sal_1_4ul_1__IL6807-715-520


title: single neuron, striatum, A2_1000701204-OGC16-sal_1_6ul_1__IL6985-706-508


title: single neuron, striatum, A3_1000701201-OGC16-sal_1_6ul_1__IL6882-729-518


title: single neuron, striatum, A3_1000701204-OGC16-sal_1_4ul_1__IL6985-707-508


title: single neuron, striatum, A3_1000701001-OGC14-sal_1_8ul_1__IL6882-707-515


title: single neuron, striatum, A2_1000700602-OGC11-sal_1_8ul_1__IL6807-714-520


title: single neuron, striatum, A1_1000701001-OGC14-sal_1_6ul_1__IL6882-705-515


title: single neuron, striatum, A2_1000701201-OGC16-sal_1_4ul_1__IL6882-728-518


title: single neuron, striatum, A1_1000701201-OGC16-sal_1_2ul_1__IL6882-727-518


title: single neuron, striatum, A11_1000700101-OGC9-sal_1_14ul_1__IL6807-705-502


title: single neuron, striatum, A10_1000701204-OGC16-sal_1_4ul_1__IL6985-716-508


title: single neuron, striatum, A4_1000701201-OGC16-sal_1_4ul_1__IL6882-701-508


title: single neuron, striatum, A10_1000700602-OGC11-sal_1_18ul_1__IL6807-722-520


title: single neuron, striatum, A12_1000701001-OGC14-sal_1_4ul_1__IL6882-715-515


title: single neuron, striatum, A10_1000700401-OGC7-coc_1_10ul_1__IL6778-714-508


title: single neuron, striatum, A2_1000701001-OGC14-sal_1_4ul_1__IL6882-706-515


title: single neuron, striatum, A12_1000700602-OGC11-sal_1_6ul_1__IL6807-724-520


title: single neuron, striatum, A11_1000701201-OGC16-sal_1_6ul_1__IL6882-710-508


title: single neuron, striatum, A09_1000700401-OGC7-coc_1_14ul_1__IL6807-702-506


title: single neuron, striatum, A4_1000700102-OGC9-sal_1_6ul_1__IL6983-703-502


title: single neuron, striatum, A11_1000700401-OGC7-coc_1_18ul_1__IL6778-715-508


title: single neuron, striatum, A11_1000700602-OGC11-sal_1_12ul_1__IL6807-723-520


title: single neuron, striatum, A10_1000700102-OGC9-sal_1_6ul_1__IL6983-707-502


title: single neuron, striatum, A11_1000701001-OGC14-sal_1_4ul_1__IL6882-714-515


title: single neuron, striatum, A07_1000700101-OGC9-sal_1_30ul_1__IL6778-706-502


title: single neuron, striatum, A04_1000700401-OGC7-coc_1_14ul_1__IL6807-727-516


title: single neuron, striatum, A07_1000700401-OGC7-coc_1_14ul_1__IL6807-701-506


title: single neuron, striatum, A12_1000701204-OGC16-sal_1_4ul_1__IL6985-719-508


title: single neuron, striatum, A10_1000700101-OGC9-sal_1_22ul_1__IL6778-710-502


title: single neuron, striatum, A04_1000700101-OGC9-sal_1_18ul_1__IL6807-702-502


title: single neuron, striatum, A06_1000700401-OGC7-coc_1_12ul_1__IL6807-729-516


title: CTV1-RNA_PU1mut_2

city: Regensburg

first: Michael

last: Rehli

address: F.-J.-Strauss-Allee 11

department: Internal Med III

country: Germany

institute: University Hospital Regensburg

data_processing:
Sequence reads were trimmed to 75bp if longer using HOMER (homerTools trim)
Sequencing reads were mapped to the human genome using STAR v2.5.3a (Dobin et al., 2013). The human hg19 genome index incorporated gene annotation from GENCODE ((Frankish et al., 2019), release 19) was used to aid in spliced alignment
Tables of raw uniquely mapped read counts per human gene were generated during mapping using the built-in --quantMode GeneCounts option in STAR.
Genome_build: hg19
Supplementary_files_format_and_content: Tab delimited text files containing the raw count values for each sample.

organism: Homo sapiens

growth_protocol: CTV-1 were cultured in RPMI 1640 (Gibco; routinely supplemented with 2 mM L-glutamine (Biochrom), 1 mM sodium pyruvate (Sigma), 50 U/ml penicillin/streptomycin, 0.4x vitamins (Sigma), 1x non-essential amino acids (Sigma), 50 μM b-mercaptoethanol (Gibco)) supplemented with 10% heat inactivated fetal bovine serum.

extract_protocol:
Total RNA was isolated with the RNeasy Mini Kit (Qiagen).
RNAseq was carried out using the using the ScriptSeq Complete Kit (Illumina) according to manufacturer’s instructions.

treatment_protocol: Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA)  and total RNA was isolated after 24 h

tag: cell line

tag: cell type

value: T cell leukemia cell line

tag: transfected ivt mrna


title: single neuron, striatum, A05_1000700101-OGC9-sal_1_38ul_1__IL6807-703-502


title: single neuron, striatum, A10_1000701201-OGC16-sal_1_4ul_1__IL6882-707-508


title: single neuron, striatum, A02_1000700101-OGC9-sal_1_30ul_1__IL6778-701-502


title: single neuron, striatum, A02_1000700401-OGC7-coc_1_22ul_1__IL6778-704-508


title: K-562_gDNA-ChIP

description: Genomic DNA (control)

library_source: genomic

data_processing:
Raw data were aligned to the human genome (GRCh37/hg19) using bowtie2 (Langmead and Salzberg, 2012) in very sensitive mode, keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10).
Bigwigs of ChIPseq data sets were generated using HOMER v4.9 (Heinz et al, 2010) and standard settings. For cancer cell lines, we used the Control-FREEC v11.0 program to determine allelic imbalances from low-depth whole genome sequencing data and corrected ChIP-seq read counts accordingly to generate CNV-corrected bigWigs.
ChIP-seq peaks were called using HOMER?s findPeaks program in ??factor?? mode using default parameters (standard) or with -fdr 0.00001 (stringent) to identify focal peaks. Stringent peaks were further filtered for a minimal normalized tag count of 15 tags per peak. All peak sets were filtered by subtracting blacklisted genomic regions 49, and by filtering out regions with a mappability <0.8. The latter was annotated to peak regions from mappability tracks generated with the GEM package using HOMER?s annotatePeaks.pl.
Genome_build: hg19
Supplementary_files_format_and_content: ChIPseq tracks in bigWig format (before and after CNV normalization
Supplementary_files_format_and_content: ChIPseq peaks (called using standard or stringent parameters)

molecule: genomic DNA

growth_protocol:
Cells were cultured in RPMI 1640 (Gibco; routinely supplemented with 2 mM L-glutamine (Biochrom), 1 mM sodium pyruvate (Sigma), 50 U/ml penicillin/streptomycin, 0.4x vitamins (Sigma), 1x non-essential amino acids (Sigma), 50 μM b-mercaptoethanol (Gibco)) supplemented with 10% heat inactivated fetal bovine serum.
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).

extract_protocol:
ChIPseq was essentially done as described (Pham et al. 2012).
Libraries were generated as described (Pham et al. 2012)

tag: tissue/cell type

value: chronic myeloid leukemia in blast crisis cell line

tag: chip antibody


title: THP-1_gDNA-ChIP

description: Genomic DNA (control)

value: acute monocytic leukemia cell line


title: U-937_gDNA-ChIP

description: Genomic DNA (control)

value: histiocytic lymphoma cell line


title: THP-1-PMAVD3_Input-ChIP

description: Chromatin IP against PU.1

growth_protocol:
Cells were cultured in RPMI 1640 (Gibco; routinely supplemented with 2 mM L-glutamine (Biochrom), 1 mM sodium pyruvate (Sigma), 50 U/ml penicillin/streptomycin, 0.4x vitamins (Sigma), 1x non-essential amino acids (Sigma), 50 μM b-mercaptoethanol (Gibco)) supplemented with 10% heat inactivated fetal bovine serum. For differentiation of THP-1 cells into macrophage-like cells PMA (10-8 M; Calbiochem) and 1,25-dihydroxyvitamin D3 (VD3, 10-7 M; Sigma) were added, cells were incubated for 3 days at 37°C, 5% CO2, 95% humidity and adherent cells were detached using Accutase solution (Sigma).
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).

value: acute monocytic leukemia cell line treated with PMA and Vitamin D3


title: THP-1_Input-ChIP

description: Chromatin IP against PU.1


title: U-937_PU.1-ChIP

description: Chromatin IP against PU.1

value: PU.1 (Santa Cruz, #sc-352X)


title: THP-1-PMAVD3_PU.1-ChIP

description: Chromatin IP against PU.1


title: ML-2_gDNA-ChIP

description: Genomic DNA (control)

value: acute myelomonocytic leukemia cell line


title: CTV1-RNA_woPU1_2


title: single neuron, striatum, A08_1000700401-OGC7-coc_1_12ul_1__IL6778-711-508


title: NB-4_PU.1-ChIP

description: Chromatin IP against PU.1

value: acute promyelocytic leukemia cell line


title: DC66h_PU.1-ChIP_donorI

description: Chromatin IP against PU.1

growth_protocol:
Peripheral blood monocytes were separated by leukapheresis of healthy donors followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge (Beckman Instruments) as previously described. Supernatants of monocyte cultures were routinely collected and analysed for the presence of interleukin 6, which was usually low, indicating that monocytes were not activated before or during elutriation. To generate immature dendritic cells, 1×10^6 monocytes/ml were cultured in RPMI 1640 medium (Gibco) supplemented with 10% fetal calf serum (FCS; Biowhittaker, Verviers, Belgium), 20 U/ml IL-4 (Promokine, Heidelberg, Germany) and 280 U/ml GM-CSF (Berlex, Seattle, USA).
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).

tag: donr id

value: donorI

value: MO-derived

tag: cell subtype

value: primary monocyte-derived dendritic cells


title: KG-1_gDNA-ChIP

description: Genomic DNA (control)

value: acute myeloid leukemia cell line


title: DC42h_PU.1-ChIP_donorK

description: Chromatin IP against PU.1

value: donorK


title: single neuron, striatum, A08_1000700101-OGC9-sal_1_38ul_1__IL6778-707-502

value: striatum

value: male


title: CTV1-RNA_PU1_2


title: EM-3_gDNA-ChIP

description: Genomic DNA (control)


title: DC18h_Input-ChIP_donorK

description: Chromatin input (control)


title: DC7d_PU.1-ChIP_donorI

description: Chromatin IP against PU.1


title: ML-2_PU.1-ChIP

description: Chromatin IP against PU.1


title: DC18h_Input-ChIP_donorI

description: Chromatin input (control)


title: DC7d_PU.1-ChIP_donorK

description: Chromatin IP against PU.1


title: NB-4_gDNA-ChIP

description: Genomic DNA (control)


title: MO_PU.1-ChIP_donorI

description: Chromatin IP against PU.1

growth_protocol:
Peripheral blood monocytes were separated by leukapheresis of healthy donors, followed by density gradient centrifugation over Ficoll/Hypaque and subsequent counter current centrifugal elutriation in a J6M-E centrifuge (Beckman, München, Germany).
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).

value: peripheral blood

value: primary monocytes


title: KG-1_PU.1-ChIP

description: Chromatin IP against PU.1


title: DC42h_PU.1-ChIP_donorI

description: Chromatin IP against PU.1


title: DC27h_PU.1-ChIP_donorK

description: Chromatin IP against PU.1


title: Artificial CD8 2

city: Bethesda

first: Li

last: Jia

state: MD

address: 10 Clinic center

institute: NCI/NIH

description:
OP9_CD8SP_2
RNA-seq data from OP9CD8 cell

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm9 whole genome using Star v2.4.2, data quantification was used Subread to get the read counts.
TMM and EdgeR were used on normalization and differential expression analysis, respectively.
Genome_build: mm9 (MGSCv37)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include raw count and normalized values for each sample.

source_name: Pmel iPSC

growth_protocol: Differentiation on OP9-DL1.

extract_protocol:
Collected by FACS based on CD45, CD4, CD8, TCR.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: iPSC

value: CD8+ T cells

tag: sample type

value: differentiated


title: Artificial CD8 4

description:
OP9_CD8SP_4
RNA-seq data from OP9CD8 cell


title: EM-3_PU.1-ChIP

description: Chromatin IP against PU.1

value: chronic myeloid leukemia in blast crisis cell line


title: DC18h_PU.1-ChIP_donorK

description: Chromatin IP against PU.1


title: Artificial CD8 5

description:
OP9_CD8SP_5
RNA-seq data from OP9CD8 cell


title: DC18h_PU.1-ChIP_donorI

description: Chromatin IP against PU.1


title: BC_PU.1-ChIP_donorC

description: Chromatin IP against PU.1

growth_protocol:
Peripheral blood mononuclear cells were isolated from leukapheresis products of healthy volunteers by density gradient centrifugation over Ficoll/Hypaque (Biochrom AG, Berlin, Germany). CD4+ cells were enriched using magnetically labeled human CD4 MicroBeads (Miltenyi Biotec, Bergisch Gladbach, Germany) and the Midi-MACS system (Miltenyi Biotec).  CD19+ cells were enriched from the CD8- fraction using magnetically labeled human CD19 MicroBeads (Miltenyi). Enriched cells were stained with CD3 FITC (BD, Klon SK7, 345763), CD19 PE (BD, Klon 4G7, 345777) and sorted for CD3+CD19+ B cells .
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).

value: donorC

value: primary B cells


title: MO_PU.1-ChIP_donorK

description: Chromatin IP against PU.1

value: PU.1 (Santa Cruz, #sc-352X)


title: CD4+CD8+ 3

description:
immature_S12
RNA-seq data from immature

value: CD4+CD8+ T cells


title: iRTE 2

description:
matureB
RNA-seq data from mature


title: Artificial CD8 1

description:
OP9_CD8SP_1
RNA-seq data from OP9CD8 cell


title: CD4+CD8+ 1

description:
immature_S10
RNA-seq data from immature


title: splenic CD8 5

description:
pmel_T_naive_5
RNA-seq data from T naïve cell

source_name: Transgenic mice

value: Spleen

value: naive CD8+ T cells

value: ex vivo


title: splenic CD8 4

description:
pmel_T_naive_4
RNA-seq data from T naïve cell


title: BC_PU.1-ChIP_donorA

description: Chromatin IP against PU.1

value: donorA


title: splenic CD8 2

description:
pmel_T_naive_2
RNA-seq data from T naïve cell


title: iRTE 5

description:
pmel_iRTE_5
RNA-seq data from mature


title: CTV-1_mutPU.1mRNA_FA_FLAG-ChIP_11

description: Chromatin IP against FLAG-epitope, 8h after mRNA transfection

source_name: T cell leukemia cell line

growth_protocol: CTV-1 and HEP-G2 cells were cultured in RPMI 1640 (Gibco; routinely supplemented with 2 mM L-glutamine (Biochrom), 1 mM sodium pyruvate (Sigma), 50 U/ml penicillin/streptomycin, 0.4x vitamins (Sigma), 1x non-essential amino acids (Sigma), 50 μM b-mercaptoethanol (Gibco)) supplemented with 10% heat inactivated fetal bovine serum; For TALL-1 cells the culture medium was supplemented with 15% heat inactivated fetal bovine serum was used; adherent HEP-G2 cells were detached using Trypsin-EDTA (Gibco)

extract_protocol:
Lysates were  preparated from sonicated nuclei and protein/histone-DNA complexes were isolated with antibody.
ChIP construction was essentially done as described (Pham et al. 2012) with slight modifications for BRG1, ETS1 and FLI1 samples, which were prepared using dual crosslinking with 2 mM DSG (Thermo Fisher Scientific) and 1% formaldehyde. Libraries for sequencing were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to manufacturer’s instructions.

treatment_protocol: Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA, PU1-delA-IVT-mRNA, PU1-delQ-IVT-mRNA, PU1-delP-IVT-mRNA, PU1-delAQP-IVT-mRNA) and cultured for 8 hours prior to chromatin extraction

value: FLAG M2 (Sigma, #F3165)

tag: fixation method

value: FA

tag: preperation batch


title: CTV-1_mutPU.1mRNA_DSG_FA_BRG1-ChIP_12


title: CTV-1_mutPU.1mRNA_DSG_FA_BRG1-ChIP_11


title: CTV1-RNA_PU1_rep_3

growth_protocol: CTV-1 were cultured in RPMI 1640 (Gibco; routinely supplemented with 2 mM L-glutamine (Biochrom), 1 mM sodium pyruvate (Sigma), 50 U/ml penicillin/streptomycin, 0.4x vitamins (Sigma), 1x non-essential amino acids (Sigma), 50 μM b-mercaptoethanol (Gibco)) supplemented with 10% heat inactivated fetal bovine serum and subjected to 7 cycles of PU.1 mRNA transfection delivering one dose a day for a total of 7 days prior to total RNA isolation.

treatment_protocol: Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA)  daily for seven days prior to RNA isolation

value: T cell leukemia cell line


title: splenic CD8 3

description:
pmel_T_naive_3
RNA-seq data from T naïve cell


title: CTV1-RNA_PU1mut_rep_3


title: iRTE 3

description:
matureC
RNA-seq data from mature


title: iRTE 1

description:
matureA
RNA-seq data from mature


title: single neuron, striatum, C10_1000701201-OGC16-sal_1_4ul_1__IL6882-706-520

value: striatum

value: male


title: iRTE 4

description:
pmel_iRTE_10
RNA-seq data from mature

value: iPSC


title: CD4+CD8+ 2

description:
immature_S11
RNA-seq data from immature


title: CTV1-RNA_woPU1_1


title: CTV-1_mutPU.1mRNA_FA_FLAG-ChIP_12


title: Artificial CD8 3

description:
OP9_CD8SP_3
RNA-seq data from OP9CD8 cell

value: CD8+ T cells


title: CTV-1_PU.1-delQmRNA_FA_FLAG-ChIP_12


title: CTV1-RNA_PU1mut_1


title: CTV-1_PU.1mRNA_FA_FLAG-ChIP_12


title: splenic CD8 1

description:
pmel_T_naive_1
RNA-seq data from T naïve cell


title: CTV-1_PU.1mRNA_FA_FLAG-ChIP_11


title: CTV-1_PU.1-delQmRNA_DSG_FA_BRG1-ChIP_11


title: CTV-1_PU.1-BirAmRNA_FA_PU.1-ChIP_10

description: Chromatin IP against PU.1, 5h after mRNA transfection


title: CTV-1_PU.1-delAmRNA_FA_FLAG-ChIP_12


title: CTV-1_PU.1-delAmRNA_FA_FLAG-ChIP_11


title: CTV-1_PU.1mRNA_DSG_FA_BRG1-ChIP_12


title: CTV-1_PU.1-delA-BirAmRNA_FA_PU.1-ChIP_10


title: CTV-1_PU.1-delQmRNA_FA_FLAG-ChIP_11


title: CTV1-RNA_PU1_1


title: CTV-1_PU.1-delQ-BirAmRNA_FA_PU.1-ChIP_10


title: CTV-1_PU.1-delAmRNA_FA_FLAG-ChIP_2


title: CTV-1_PU.1mRNA_DSG_FA_BRG1-ChIP_11


title: CTV1_PU1_delQ_7

description: Cells were transfected with IVT mRNA and transposition was carried out 8 hours after transfection

data_processing:
Raw data were aligned to the human genome (GRCh37/hg19) using bowtie2 in very-sensitive and no-discordant modes, keeping only reads that map to a single unique genomic location for further analysis (MAPQ > 10). Read positions were adjusted to move the ends proximal to the Tn5 binding site (for reads on the positive strand, the start is shifted +4 bp and its partner reads start -5 bp, for reads on the negative strand, the start is shifted -5 bp and its partner reads start +4 bp) using a custom script.
Bigwigs of ChIPseq data sets were generated using HOMER v4.9 (Heinz et al, 2010) and a fixed fragment length of 65 bp. For cancer cell lines, we used the Control-FREEC v11.0 program to determine allelic imbalances from low-depth whole genome sequencing data and corrected ChIP-seq read counts accordingly to generate CNV-corrected bigWigs.
ATAC-seq peak regions were called by combining two different approaches: The basic peak region set was called using HOMER?s findPeaks program in ?region?? mode using parameters ?-size 150 -minDist 250 -L 2 -fdr 0.00001? to identify regions of variable length by stitching nucleosome-size peaks. To exclude shallow peak regions, only those were kept that overlapped a second peak set that was generated in ??factor?? mode using parameters ?-size 250 -minDist 250 -L 2 -fdr 0.00001? to identify focal peaks.
Genome_build: hg19hg19
Supplementary_files_format_and_content: coverage tracks in bigWig format (before and after CNV normalization
Supplementary_files_format_and_content: ATACseq peaks (open chromatin regions)

extract_protocol:
Cells were treated with DNase I directly in culture medium prior to nuclear transposition procedure.
ATACseq was  essentially done as described (Corces et al. 2017).

treatment_protocol: Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA, PU1-delA-IVT-mRNA) and cultured for 8 hours prior to lysis procedure.

tag: molecule subtype

value: transposed, nuclear DNA


title: CTV-1_mock_FA_FLAG-ChIP_1

description: Chromatin IP against FLAG-epitope, 8h after mock transfection (no RNA)


title: CTV1_PU1_delA_6


title: CTV1_PU1_7


title: CTV-1_PU.1-delQmRNA_FA_FLAG-ChIP_1


title: CTV-1_PU.1-delAmRNA_DSG_FA_BRG1-ChIP_12


title: CTV-1_gDNA

description: Chromatin input (control)


title: CTV-1_PU.1-delAmRNA_DSG_FA_BRG1-ChIP_11


title: CTV1_PU1_delA_7


title: CTV-1_PU.1-delPmRNA_FA_FLAG-ChIP_2


title: HepG2_mutPU.1mRNA_FA_FLAG-ChIP_2

value: hepatocellular carcinoma cell line


title: CTV-1_PU.1-delPmRNA_FA_FLAG-ChIP_1


title: CTV-1_PU.1-delQmRNA_DSG_FA_BRG1-ChIP_12


title: HepG2_mutPU.1mRNA_FA_FLAG-ChIP_1


title: ciona_sperm

city: beijing

first: jiang

last: liu

address: NO.1 Beichen West Road, Chaoyang District

country: China

institute: Beijing Institute of Genomics, Chinese Academy of Sciences

description: 3 replicates;replicate1[ciona_sperm_rep1_*.fastq.gz];replicate2[ciona_sperm_rep2_*.fastq.gz];replicate3[ciona_sperm_rep3_*.fastq.gz]

data_processing:
Adapters and low-quality reads were trimed with Trimmomatic
Reads alignment were performed with Bismark with default settings
duplicates were removed by deduplicate_bismark function of Bismark, and overlapped part of paired-end reads were removed by clipOverlap of bamUtil_1.0.9
methylation level were extracted with mpileup function of Samtools (v0.1.19)
Genome_build: sea_anemone[ASM20922v1];honey_bee[GCA_000002195.1];sea_urchin[Spur_3.1];ciona[CSAV2.0]
Supplementary_files_format_and_content: Format: bed; content: Methylation level for each CpG site plus 2 columns representing the numbers of Cs and Ts

organism: Ciona savignyi

source_name: Ciona sperm

extract_protocol:
The gametes and embryos were frozen at 70 below zero or subjected to immediate genomic extraction procedures.  Genomic DNA was extracted by QIAamp DNA Mini Kit(QIAGEN) following the protocol of DNA Purification from Tissues with the cell lysis time adjusted depending on different samples.
Genomic DNA spiked with 0.5％ unmethylated Lambda DNA (Promega) was sonicated into 100-500bp. Fragmented DNA was then subjected to end repair,dA tailing, ligation with the end repair enzyme mix (NEB),  Klenow 3´-5´ exo- (NEB) and  T4 DNA ligase (NEB), respectively. Adapter-ligated DNA was recovered by 2％ agarose gel electrophoresis, and bisulfite conversion was performed using the EZ DNA methylation-Gold kit (Zymo Research) according to the instruction manual. Bisulfite-treated DNA was amplified with KAPA HiFi HotStart Uracil+ ReadyMix. Amplified DNA  was recovered by 2％ agarose gel electrophoresis.

value: sperm

tag: developmental stage

value: gamete


title: HepG2_PU.1mRNA_FA_FLAG-ChIP_2


title: CTV-1_PU.1-delAQPmRNA_FA_FLAG-ChIP_2


title: CTV-1_mutPU.1mRNA_FA_Input-ChIP_1

description: Chromatin input (control)


title: CTV-1_PU.1-delAQPmRNA_FA_FLAG-ChIP_1


title: CTV1_PU1_delQ_6


title: TALL1_gDNA

description: Genomic DNA (control)


title: TALL1_mutPU.1mRNA_FA_FLAG-ChIP_1


title: HepG2_PU.1mRNA_FA_FLAG-ChIP_1


title: CTV-1_mutPU.1mRNA_FA_H3K27ac-ChIP_3

description: Chromatin IP against H3K27ac, 8h after mRNA transfection

value: H3K27ac (Abcam, #ab4729)


title: CTV-1_PU.1-delQmRNA_FA_FLAG-ChIP_2


title: CTV-1_mutPU.1mRNA_FA_H3K27ac-ChIP_2


title: CTV-1_mutPU.1mRNA_FA_H3K27ac-ChIP_1


title: CTV1_PU1mut_7


title: CTV-1_PU.1-delAmRNA_DSG_FA_BRG1-ChIP_4

description: Chromatin IP against BRG1, 8h after mRNA transfection


title: ciona_gastrula

description: 2 replicates;replicate1[ciona_gastrula_rep1_*.fastq.gz];replicate2[ciona_gastrula_rep2_*.fastq.gz]

source_name: Ciona gastrula

value: gastrula

value: embryo


title: CTV1_PU1mut_6


title: CTV-1_mutPU.1mRNA_DSG_FA_Input-ChIP_5

description: Chromatin input (control)


title: honey_bee_oocyte

description: 2 replicates;replicate1[honey_bee_oocyte_rep1_*.fastq.gz];replicate2[honey_bee_oocyte_rep2_*.fastq.gz]

organism: Apis mellifera

source_name: honey_bee oocyte

value: oocyte


title: ciona_cleavage

description: 3 replicates;replicate1[ciona_cleavage_rep1_*.fastq.gz];replicate2[ciona_cleavage_rep2_*.fastq.gz];replicate3[ciona_cleavage_rep3_*.fastq.gz]

source_name: Ciona cleavage

value: cleavage


title: HepG2_gDNA

description: Genomic DNA (control)


title: ciona_oocyte

description: 3 replicates;replicate1[ciona_oocyte_rep1_*.fastq.gz];replicate2[ciona_oocyte_rep2_*.fastq.gz];replicate3[ciona_oocyte_rep3_*.fastq.gz]

source_name: Ciona oocyte


title: CTV1_PU1_6


title: honey_bee_drone_gastrula

description: 2 replicates;replicate1[honey_bee_drone_gastrula_rep1_*.fastq.gz];replicate2[honey_bee_drone_gastrula_rep2_*.fastq.gz]

source_name: honey_bee drone gastrula

value: Drone gastrula


title: CTV-1_mutPU.1mRNA_FA_FLAG-ChIP_3

value: FLAG M2 (Sigma, #F3165)


title: CTV-1_mutPU.1mRNA_DSG_FA_FLI1-ChIP_8

description: Chromatin IP against FLI1, 8h after mRNA transfection

value: FLI1 (Abcam, #ab15289)


title: sea_anemone_blastula_MA

description: sampled from Massachusetts;1 replicate

organism: Nematostella vectensis

source_name: sea_anemone blastula embryo

value: blastula


title: CTV-1_PU.1-delAmRNA_FA_FLAG-ChIP_1

value: T cell leukemia cell line

value: FA


title: TALL1_mutPU.1mRNA_FA_FLAG-ChIP_2


title: TALL1_PU.1mRNA_FA_FLAG-ChIP_2


title: honey_bee_drone_blastoderm

description: 2 replicates;replicate1[honey_bee_drone_blastoderm_rep1_*.fastq.gz];replicate2[honey_bee_drone_blastoderm_rep2_*.fastq.gz]

source_name: honey_bee drone blastoderm

value: drone blastoderm


title: TALL1_PU.1mRNA_FA_FLAG-ChIP_1

description: Chromatin IP against FLAG-epitope, 8h after mRNA transfection


title: CTV-1_PU.1-delAmRNA_DSG_FA_BRG1-ChIP_5


title: CTV-1_mutPU.1mRNA_FA_FLAG-ChIP_5


title: honey_bee_worker_blastoderm

description: 2 replicates;replicate1[honey_bee_worker_blastoderm_rep1_*.fastq.gz];replicate2[honey_bee_worker_blastoderm_rep2_*.fastq.gz]

source_name: honey_bee worker blastoderm

value: Worker blastoderm


title: CTV-1_PU.1-delAmRNA_FA_FLAG-ChIP_5


title: CTV-1_mutPU.1mRNA_FA_FLAG-ChIP_4


title: CTV-1_PU.1-delAmRNA_FA_FLAG-ChIP_4


title: CTV-1_mutPU.1mRNA_DSG_FA_BRG1-ChIP_5


title: honey_bee_sperm

description: 2 replicates;replicate1[honey_bee_sperm_rep1_*.fastq.gz];replicate2[honey_bee_sperm_rep2_*.fastq.gz]

source_name: honey_bee sperm


title: CTV-1_mutPU.1mRNA_FA_PU.1-ChIP_2

description: Chromatin IP against PU.1, 8h after mRNA transfection

value: PU.1 (Santa Cruz, #sc-352X)


title: CTV-1_mutPU.1mRNA_FA_PU.1-ChIP_1


title: CTV-1_mutPU.1mRNA_DSG_FA_BRG1-ChIP_4


title: CTV-1_PU.1mRNA_DSG_FA_Input-ChIP_5

description: Chromatin input (control)


title: CTV-1_PU.1mRNA_FA_FLAG-ChIP_PFI3_10uM_7

treatment_protocol:
The small molecule inhibitor PFI-3 was used to selectively inhibit the SMARCA4/2 polybromo 1 domain of the SWI/SNF complex. Therefore PU.1 IVT mRNA-transfected CTV-1 cells were cultured in RPMI 1640 (Gibco; routinely supplemented with 2 mM L-glutamine (Biochrom), 1 mM sodium pyruvate (Sigma), 50 U/ml penicillin/streptomycin, 0.4x vitamins (Sigma), 1x non-essential amino acids (Sigma), 50 μM b-mercaptoethanol (Gibco)) supplemented with 10% heat inactivated fetal bovine serum containing  10 µM PFI-3. Chromatin was harvested 8 hours after transfection and treatment.
Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA, PU1-delA-IVT-mRNA, PU1-delQ-IVT-mRNA, PU1-delP-IVT-mRNA, PU1-delAQP-IVT-mRNA) and cultured for 8 hours prior to chromatin extraction


title: sea_anemone_gastrula_FL

description: sampled from Florida;2 replicates;replicate1[sea_anemone_gastrula_FL_rep1*fastq.gz];replicate2[sea_anemone_gastrula_FL_rep2*fastq.gz]

source_name: sea_anemone gastrula embryo


title: sea_anemone_oocyte_FL

description: sampled from Florida;1 replicate

source_name: sea_anemone oocyte


title: CTV-1_mutPU.1mRNA_DSG_FA_FLI1-ChIP_9


title: CTV-1_mutPU.1mRNA_FA_PU.1-ChIP_3


title: CTV-1_mutPU.1mRNA_DSG_FA_ETS1-ChIP_9

description: Chromatin IP against ETS1, 8h after mRNA transfection

value: ETS1 (Santa Cruz, #sc-350X)


title: CTV-1_mutPU.1mRNA_DSG_FA_ETS1-ChIP_8


title: CTV-1_mutPU.1mRNA_FA_FLAG-ChIP_2


title: sea_anemone_blastula_FL

description: sampled from Florida;1 replicate


title: CTV-1_PU.1mRNA_DSG_FA_BRG1-ChIP_4


title: sea_anemone_cleavage_MA

description: sampled from Massachusetts;1 replicate

source_name: sea_anemone cleavage embryo


title: sea_anemone_cleavage_FL

description: sampled from Florida; 2 replicates;replicate1[sea_anemone_cleavage_FL_rep1*fastq.gz];replicate2[sea_anemone_cleavage_FL_rep2*fastq.gz,sea_anemone_cleavage_FL_rep3*fastq.gz]


title: sea_anemone_sperm_FL

description: sampled from Florida;1 replicate

source_name: sea_anemone sperm

value: sperm


title: TRP_N20_rep2

city: Berkeley

first: Xavier

last: Darzacq

state: CA

address: 475D Li Ka Shing Center

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Base-calling performed with CASAVA by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley
ChIP-seq reads were aligned to the mm10 genome assembly using bowtie2 with --very-sensitive-local
bigWig coverage files were generated with deepTools with the following configurations: --binSize 10 --normalizeUsing RPGC --effectiveGenomeSize 2308125349 --ignoreDuplicates --ignoreForNormalization chrX chrY chrM
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files

source_name: embryonic stem cells

growth_protocol: JM8.N4 mouse embryonic stem cells were grown on plates pre-coated with a 0.1% autoclaved gelatin solution (Sigma-Aldrich, G9391) under feeder free condition in knock-out DMEM with 15% FBS and LIF (full recipe: 500 mL DMEM (ThermoFisher#10829018), 6 mL MEM NEAA (ThermoFisher #11140050), 6 mL GlutaMax (ThermoFisher#35050061), 5 mL Penicillin-streptomycin (ThermoFisher #15140122), 4.6 μL 2-mercapoethanol (Sigma-Aldrich M3148), 90 mL fetal bovine serum (HyClone FBS SH30910.03 lot #AXJ47554)). mES cells were fed by replacing half the medium with fresh medium daily and passaged every two days by trypsinization.

extract_protocol:
Cell pellets were thawed in ice and resuspended in cell lysis buffer (5 mM PIPES, pH 8.0, 85 mM KCl, and 0.5% NP-40, 1 ml/15 cm plate) and incubated for 10 min on ice. Lysates were then centrifuged for 10 min at 4000 rpm. Nuclear pellets were resuspended in 6 volumes of sonication buffer (50 mM Tris-HCl, pH 8.1, 10 mM EDTA, 0.1% SDS), incubated on ice for 10 min, and sonicated to obtain DNA fragments below 2000 bp in length (Covaris S220 sonicator, 20% Duty factor, 200 cycles/burst, 100 peak incident power, 25 cycles of 20" on and 40" off). Sonicated lysates were cleared by centrifugation and 1 mg of chromatin was diluted in RIPA buffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 140 mM NaCl) to a final concentration of 0.8 μg/μl, precleared with Protein A sepharose (GE Healthcare) for 2 hours at 4°C and immunoprecipitated overnight with 10 μg of antibodies. 4% of the precleared chromatin was saved as input. Immunoprecipitated DNA was purified with the Qiagen QIAquick PCR Purification Kit, eluted in 40 μl of water and used for library preparation.
Solexa rapid prep (see linked manuscript).

treatment_protocol: Cells were treated with 1 µM triptolide (in DMSO) for 45 minutes and cross-linked for 6 minutes at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final). Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10 min at 4000 rpm, 4 'C and pellets flash-frozen in liquid nitrogen and stored at - 80 'C until lysed.

value: embryonic stem cells

tag: genotype/variation

value: Wild-type with Tripotolide treatment

value: anti-Pol II (Polr2a) N-20 (Santa Cruz Biotechnology, sc-899)


title: CTV-1_PU.1mRNA_FA_DMSO_ChIP-Input_7

description: Chromatin input (control)

treatment_protocol:
The small molecule inhibitor PFI-3 was used to selectively inhibit the SMARCA4/2 polybromo 1 domain of the SWI/SNF complex. As control PU.1 IVT mRNA-transfected CTV-1 cells were cultured in RPMI 1640 (Gibco; routinely supplemented with 2 mM L-glutamine (Biochrom), 1 mM sodium pyruvate (Sigma), 50 U/ml penicillin/streptomycin, 0.4x vitamins (Sigma), 1x non-essential amino acids (Sigma), 50 μM b-mercaptoethanol (Gibco)) supplemented with 10% heat inactivated fetal bovine serum containing the DMSO. Chromatin was harvested 8 hours after transfection and treatment.
Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA, PU1-delA-IVT-mRNA, PU1-delQ-IVT-mRNA, PU1-delP-IVT-mRNA, PU1-delAQP-IVT-mRNA) and cultured for 8 hours prior to chromatin extraction


title: CTV-1_mutPU.1mRNA_FA_FLAG-ChIP_1


title: CTV-1_PU.1mRNA_DSG_FA_ETS1-ChIP_9


title: FLV_input_rep2

treatment_protocol: Cells were treated with 2 µM flavopiridol (in DMSO) for 45 minutes and cross-linked for 6 minutes at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final). Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10 min at 4000 rpm, 4 'C and pellets flash-frozen in liquid nitrogen and stored at - 80 'C until lysed.

value: Wild-type with Flavopiridol treatment


title: TRP_input_rep2


title: FLV_N20_rep2


title: CTV-1_PU.1mRNA_DSG_FA_BRG1-ChIP_5


title: TRP_N20_rep1


title: sea_anemone_sperm_MA

description: sampled from Massachusetts;1 replicate

value: gamete


title: CTV-1_PU.1mRNA_FA_FLAG-ChIP_PFI3_5uM_7

treatment_protocol:
The small molecule inhibitor PFI-3 was used to selectively inhibit the SMARCA4/2 polybromo 1 domain of the SWI/SNF complex. Therefore PU.1 IVT mRNA-transfected CTV-1 cells were cultured in RPMI 1640 (Gibco; routinely supplemented with 2 mM L-glutamine (Biochrom), 1 mM sodium pyruvate (Sigma), 50 U/ml penicillin/streptomycin, 0.4x vitamins (Sigma), 1x non-essential amino acids (Sigma), 50 μM b-mercaptoethanol (Gibco)) supplemented with 10% heat inactivated fetal bovine serum containing  5 µM PFI-3. Chromatin was harvested 8 hours after transfection and treatment.
Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA, PU1-delA-IVT-mRNA, PU1-delQ-IVT-mRNA, PU1-delP-IVT-mRNA, PU1-delAQP-IVT-mRNA) and cultured for 8 hours prior to chromatin extraction


title: TRP_input_rep1


title: CTV-1_PU.1mRNA_FA_FLAG-ChIP_PFI3_1uM_7

treatment_protocol:
The small molecule inhibitor PFI-3 was used to selectively inhibit the SMARCA4/2 polybromo 1 domain of the SWI/SNF complex. Therefore PU.1 IVT mRNA-transfected CTV-1 cells were cultured in RPMI 1640 (Gibco; routinely supplemented with 2 mM L-glutamine (Biochrom), 1 mM sodium pyruvate (Sigma), 50 U/ml penicillin/streptomycin, 0.4x vitamins (Sigma), 1x non-essential amino acids (Sigma), 50 μM b-mercaptoethanol (Gibco)) supplemented with 10% heat inactivated fetal bovine serum containing  1 µM PFI-3. Chromatin was harvested 8 hours after transfection and treatment.
Cells were transfected with the indicated in vitro transcribed mRNA transcripts (PU1-IVT-mRNA, PU1mut-IVT-mRNA, PU1-delA-IVT-mRNA, PU1-delQ-IVT-mRNA, PU1-delP-IVT-mRNA, PU1-delAQP-IVT-mRNA) and cultured for 8 hours prior to chromatin extraction


title: DMSO_N20t_rep2

treatment_protocol: Cells were treated with DMSO for 45 minutes and cross-linked for 6 minutes at room temperature with 1% formaldehyde-containing medium; cross-linking was stopped by PBS-glycine (0.125 M final). Cells were washed twice with ice-cold PBS, scraped, centrifuged for 10 min at 4000 rpm, 4 'C and pellets flash-frozen in liquid nitrogen and stored at - 80 'C until lysed.

value: Wild-type with DMSO treatment


title: CTV-1_PU.1mRNA_DSG_FA_ETS1-ChIP_8


title: DMSO_input_rep2


title: honey_bee_worker_gastrula

description: 2 replicates;replicate1[honey_bee_worker_gastrula_rep1_*.fastq.gz];replicate2[honey_bee_worker_gastrula_rep2_*.fastq.gz]

source_name: honey_bee worker gastrula

value: Worker gastrula

value: embryo


title: CTV-1_PU.1mRNA_DSG_FA_FLI1-ChIP_9

value: FLI1 (Abcam, #ab15289)


title: CTV-1_PU.1mRNA_FA_FLAG-ChIP_DMSO_7

value: FLAG M2 (Sigma, #F3165)


title: THP-1_PU.1-ChIP

description: Genomic DNA (control)

value: acute monocytic leukemia cell line


title: CTV-1_PU.1mRNA_FA_FLAG-ChIP_15perc_6

value: T cell leukemia cell line

value: FA


title: CTV-1_PU.1mRNA_FA_FLAG-ChIP_50perc_6


title: FLV_input_rep1


title: CTV-1_PU.1mRNA_FA_FLAG-ChIP_5


title: CTV-1_PU.1mRNA_FA_FLAG-ChIP_4


title: CTV-1_PU.1mRNA_FA_H3K27ac-ChIP_3

description: Chromatin IP against H3K27ac, 8h after mRNA transfection

value: H3K27ac (Abcam, #ab4729)


title: FLV_N20_rep1


title: BDMC_Input-ChIP_donorH

description: Chromatin input (control)

growth_protocol:
Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014)
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).

value: donorH

value: breast tissue

value: breast-derived primary mast cells


title: DMSO_N20_rep1

value: embryonic stem cells


title: BDMC_Input-ChIP_donorG

description: Chromatin input (control)

value: donorG


title: BDMC_PU.1-ChIP_donorH

description: Chromatin IP against PU.1

value: PU.1 (Santa Cruz, #sc-352X)


title: CTV-1_PU.1mRNA_FA_H3K27ac-ChIP_1


title: NEU_PU.1-ChIP_donorF

description: Chromatin IP against PU.1

growth_protocol:
Neutrophils were purified from whole blood after lysis of erythrocytes and purified by FACS based on size and granularity.
Collection of blood cells from healthy donors was performed in compliance with the Helsinki Declaration. All donors signed an informed consent. The leukapheresis procedure and subsequent purification of hematopoietic cell types were approved by the local ethical committee (reference number 12-101-0260). Human mast cell were purified from skin that was obtained from cosmetic breast-reduction surgeries (Motakis et al., 2014) with informed consent of the patients. Mast cell preparations were performed in compliance with the Helsinki Declaration, and approved by the ethics committee of the Charité Universitätsmedizin Berlin (reference number EA1/204/10).

value: donorF

value: peripheral blood

value: primary neutrophils


title: CTV-1_PU.1mRNA_FA_FLAG-ChIP_6


title: CTV-1_PU.1mRNA_FA_PU.1-ChIP_3


title: BDMC_PU.1-ChIP_donorG

description: Chromatin IP against PU.1


title: CTV-1_PU.1mRNA_DSG_FA_FLI1-ChIP_8


title: NEU_Input-ChIP_donorF

description: Chromatin input (control)


title: CTV-1_PU.1mRNA_FA_H3K27ac-ChIP_2


title: HEPG2_PU1mut_2

description: Cells were transfected with IVT mRNA and transposition was carried out 8 hours after transfection

value: hepatocellular carcinoma cell line

value: transposed, nuclear DNA


title: Pol2i_FLV_rep2

data_processing:
Library strategy: Micro-C
Base-calling performed with CASAVA by the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley
allValidPairs were generated by HiC-Pro package (>2.10 version)
mcool files were converted from allValidPairs by Cooler package
hic file were converted from allValidPairs by Juicer tools
Genome_build: mm10
Supplementary_files_format_and_content: allValidParis file contains 1) read name, 2) chromosome of first locus, 3) read position of first locus, 4) strand of first locus, 5) chromosome of second locus, 6) read position of second locus, 7) strand of second locus, 8) DNA fragment length, 9) name of first restriction fragment, 10) name of second restriction fragment, 11) mapping quality of first read, 12) mapping quality of second read.
Supplementary_files_format_and_content: mcool file contains all valid Micro-C pairs stored in HDF5 format with multiple resolutions
Supplementary_files_format_and_content: hic file contains all valid Micro-C pairs with multiple resolutions

extract_protocol:
Micro-C protocol was performed as the following steps: 1) digest crosslinked chromatin by MNase; 2) Repair fragment ends with biotin-dNTP; 3) Proximal ligation and purge unligated ends; 4) Purify ligated dinucleosomal DNA.
Purified DNA with biotin-dNTPs was captured by Dynabeads® MyOne™ Streptavidin C1. Standard library preparation protocol including end-repair, A-tailing, and adapter ligation was performed on beads with individual enzymes purchased from Lucigen or NEBnext UltraII kit. Sequencing library was amplified by Kapa HiFi PCR enzyme with lowest possible cycles to reduce PCR duplicates. Sequencing library was sequenced paired-end 50x50 in Illumina HiSeq 4000 sequencer.

treatment_protocol: Cells were treated with 2 µM flavopiridol (in DMSO) for 45 minutes and crosslinked by 1% formaldehyde for 10 min at room temperature. Formaldehyde reaction was quenched by 0.75M Tris. After two times of PBS washes, cells were then crosslinked by 3mM DSG for 45 min at room temperature. After two times of PBS washed, cell pellets were snap frozen or subjected to the following protocols.

value: Wild-type with Flavopiridol treatment


title: CTV-1_PU.1mRNA_FA_PU.1-ChIP_2